From dd94d03ece17a14b09f89fe3058213ee9eb666d1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Aug 2023 14:00:50 +0200 Subject: [PATCH 001/175] remove public aws ecr profile --- conf/public_aws_ecr.config | 33 --------------------------------- nextflow.config | 3 --- 2 files changed, 36 deletions(-) delete mode 100644 conf/public_aws_ecr.config diff --git a/conf/public_aws_ecr.config b/conf/public_aws_ecr.config deleted file mode 100644 index 14b577d7..00000000 --- a/conf/public_aws_ecr.config +++ /dev/null @@ -1,33 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - AWS ECR Config -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config to set public AWS ECR images wherever possible - This improves speed when running on AWS infrastructure. - Use this as an example template when using your own private registry. ----------------------------------------------------------------------------------------- -*/ - -docker.registry = 'public.ecr.aws' -podman.registry = 'public.ecr.aws' - -process { - withName: '.*:SRA_IDS_TO_RUNINFO' { - container = 'quay.io/biocontainers/python:3.9--1' - } - withName: '.*:SRA_RUNINFO_TO_FTP' { - container = 'quay.io/biocontainers/python:3.9--1' - } - withName: '.*:MULTIQC_MAPPINGS_CONFIG' { - container = 'quay.io/biocontainers/python:3.9--1' - } - withName: '.*:SRATOOLS_FASTERQDUMP' { - container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' - } - withName: '.*:SRA_MERGE_SAMPLESHEET' { - container = 'quay.io/nf-core/ubuntu:20.04' - } - withName: '.*:SYNAPSE_MERGE_SAMPLESHEET' { - container = 'quay.io/nf-core/ubuntu:20.04' - } -} diff --git a/nextflow.config b/nextflow.config index 6eb5c18d..7b693a85 100644 --- a/nextflow.config +++ b/nextflow.config @@ -159,9 +159,6 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } - public_aws_ecr { - includeConfig 'conf/public_aws_ecr.config' - } test { includeConfig 'conf/test.config' } test_synapse { includeConfig 'conf/test_synapse.config' } test_full { includeConfig 'conf/test_full.config' } From 1c5a396d686d53d58833c1be10c9b555ffb0c1e0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Aug 2023 14:06:42 +0200 Subject: [PATCH 002/175] split up config files to be more modular --- conf/modules/base.config | 32 +++++++++ conf/{modules.config => modules/sra.config} | 79 --------------------- conf/modules/synapse.config | 69 ++++++++++++++++++ nextflow.config | 4 +- 4 files changed, 104 insertions(+), 80 deletions(-) create mode 100644 conf/modules/base.config rename conf/{modules.config => modules/sra.config} (58%) create mode 100644 conf/modules/synapse.config diff --git a/conf/modules/base.config b/conf/modules/base.config new file mode 100644 index 00000000..d7eb6c86 --- /dev/null +++ b/conf/modules/base.config @@ -0,0 +1,32 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. +---------------------------------------------------------------------------------------- +*/ + +// +// Generic process options for all workflows +// +process { + + publishDir = [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + + withName: CUSTOM_DUMPSOFTWAREVERSIONS { + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: params.publish_dir_mode, + pattern: '*_versions.yml' + ] + } + +} diff --git a/conf/modules.config b/conf/modules/sra.config similarity index 58% rename from conf/modules.config rename to conf/modules/sra.config index f5cb1c77..e6e9d168 100644 --- a/conf/modules.config +++ b/conf/modules/sra.config @@ -10,27 +10,6 @@ ---------------------------------------------------------------------------------------- */ -// -// Generic process options for all workflows -// -process { - - publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } - -} - // // Process options for the SRA workflow // @@ -111,61 +90,3 @@ if (params.input_type == 'sra') { } } - -// -// Process options for the Synapse workflow -// -if (params.input_type == 'synapse') { - - process { - - withName: SYNAPSE_LIST { - ext.args = '--long' - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SYNAPSE_GET { - publishDir = [ - [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ], - [ - path: { "${params.outdir}/fastq/md5" }, - mode: params.publish_dir_mode, - pattern: "*.md5" - ] - ] - } - - withName: SYNAPSE_SHOW { - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SYNAPSE_TO_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - enabled: false - ] - } - - withName: SYNAPSE_MERGE_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - } - -} diff --git a/conf/modules/synapse.config b/conf/modules/synapse.config new file mode 100644 index 00000000..bcca94db --- /dev/null +++ b/conf/modules/synapse.config @@ -0,0 +1,69 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. +---------------------------------------------------------------------------------------- +*/ + +// +// Process options for the Synapse workflow +// +if (params.input_type == 'synapse') { + + process { + + withName: SYNAPSE_LIST { + ext.args = '--long' + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: SYNAPSE_GET { + publishDir = [ + [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ], + [ + path: { "${params.outdir}/fastq/md5" }, + mode: params.publish_dir_mode, + pattern: "*.md5" + ] + ] + } + + withName: SYNAPSE_SHOW { + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: SYNAPSE_TO_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + enabled: false + ] + } + + withName: SYNAPSE_MERGE_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + } + +} diff --git a/nextflow.config b/nextflow.config index 6eb5c18d..486c058c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -217,7 +217,9 @@ manifest { } // Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +includeConfig 'conf/modules/base.config' +includeConfig 'conf/modules/sra.config' +includeConfig 'conf/modules/synapse.config' // Function to ensure that resource requirements don't go beyond // a maximum limit From 9c5fadbd335d3f84064516d3bc1b93a06dc4baa9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Aug 2023 15:33:13 +0200 Subject: [PATCH 003/175] no cascade inclusion of config files --- conf/test.config | 3 --- nextflow.config | 5 ++++- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/test.config b/conf/test.config index 0bc98595..3c58e9cf 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,6 +22,3 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv' } - -// Load test_data.config for nf-tests -includeConfig 'test_data.config' diff --git a/nextflow.config b/nextflow.config index 7b693a85..578b233d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -159,7 +159,10 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } - test { includeConfig 'conf/test.config' } + test { + includeConfig 'conf/test.config' + includeConfig 'conf/test_data.config' + } test_synapse { includeConfig 'conf/test_synapse.config' } test_full { includeConfig 'conf/test_full.config' } } From 5073409171943f07d0248f8bc15dc2db52e13bef Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Aug 2023 15:33:46 +0200 Subject: [PATCH 004/175] use schema_ignore_params to remove warnings --- conf/test.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conf/test.config b/conf/test.config index 3c58e9cf..6a9d5d38 100644 --- a/conf/test.config +++ b/conf/test.config @@ -21,4 +21,6 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv' + + schema_ignore_params = 'fastq_ftp_ids,genomes,merge_samplesheet_ids,test_data,test_data_base' } From bc7fd25c21e1a058d00870513d1eb742847d3b0f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Aug 2023 16:21:07 +0200 Subject: [PATCH 005/175] fix lint --- .nf-core.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index 253f86e2..269ee3ed 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,5 +1,8 @@ repository_type: pipeline lint: + actions_ci: false + files_exist: + - conf/modules.config files_unchanged: - .github/CONTRIBUTING.md - .github/ISSUE_TEMPLATE/bug_report.yml @@ -7,7 +10,6 @@ lint: - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy - .gitattributes - actions_ci: false multiqc_config: false nextflow_config: - "params.validationShowHiddenParams" From 81324d23467f153484ffbb4f65f465f118d071c7 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 21 Aug 2023 18:05:36 +0100 Subject: [PATCH 006/175] Adds emit statement for FASTQs and metadata to SRA workflow --- CHANGELOG.md | 1 + .../sra_to_samplesheet/tests/main.nf.test.snap | 18 +++++++++--------- workflows/sra/main.nf | 18 ++++++++++++++---- 3 files changed, 24 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 146b93b6..8573dea7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Enhancements & fixes - [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests +- Emits all files in workflow for testing and enabling workflow to be imported when supported by Nextflow ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16 diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap index 8b5f4947..e60c646a 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -19,8 +19,8 @@ "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", "md5_1": "9fd57225d6c07a31843276d6df9b15c0", "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", "single_end": false @@ -45,8 +45,8 @@ "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", "md5_1": "9fd57225d6c07a31843276d6df9b15c0", "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", "single_end": false @@ -71,8 +71,8 @@ "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", "md5_1": "9fd57225d6c07a31843276d6df9b15c0", "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", "single_end": false @@ -97,8 +97,8 @@ "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", "md5_1": "9fd57225d6c07a31843276d6df9b15c0", "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", "single_end": false @@ -108,6 +108,6 @@ ] } ], - "timestamp": "2023-08-17T10:55:52+0000" + "timestamp": "2023-08-23T09:38:15+0000" } } \ No newline at end of file diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 512a73d4..3ca9b33e 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -81,6 +81,8 @@ workflow SRA { .set { ch_sra_metadata } ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first()) + fastq_files = Channel.empty() + if (!params.skip_fastq_download) { ch_sra_metadata @@ -111,10 +113,13 @@ workflow SRA { ) ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first()) - SRA_FASTQ_FTP - .out - .fastq - .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads) + // Isolate FASTQ channel which will be added to emit block + fastq_files = fastq_files.mix( + SRA_FASTQ_FTP.out.fastq, + FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads + ) + + fastq_files .map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] @@ -161,6 +166,11 @@ workflow SRA { CUSTOM_DUMPSOFTWAREVERSIONS ( ch_versions.unique().collectFile(name: 'collated_versions.yml') ) + + emit: + fastq = fastq_files + samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet + mapping = SRA_MERGE_SAMPLESHEET.out.mappings } /* From 82fa5000fe8a468a4e202f5765d78b12a93c7e0f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 24 Aug 2023 15:50:52 +0200 Subject: [PATCH 007/175] Update nextflow.config Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- nextflow.config | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 486c058c..6b7463d3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -218,8 +218,12 @@ manifest { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules/base.config' -includeConfig 'conf/modules/sra.config' -includeConfig 'conf/modules/synapse.config' +if ( params.input_type == 'sra' ) { + includeConfig 'conf/modules/sra.config' +} +if ( params.input_type == 'synapse' ) { + includeConfig 'conf/modules/synapse.config' +} // Function to ensure that resource requirements don't go beyond // a maximum limit From 011addc3cf5d6ad036adc435cd30eaf88df2582d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Aug 2023 15:52:05 +0200 Subject: [PATCH 008/175] remove if statement --- conf/modules/sra.config | 122 +++++++++++++++++------------------- conf/modules/synapse.config | 83 ++++++++++++------------ 2 files changed, 99 insertions(+), 106 deletions(-) diff --git a/conf/modules/sra.config b/conf/modules/sra.config index e6e9d168..15802b41 100644 --- a/conf/modules/sra.config +++ b/conf/modules/sra.config @@ -13,80 +13,76 @@ // // Process options for the SRA workflow // -if (params.input_type == 'sra') { +process { - process { - - withName: SRA_IDS_TO_RUNINFO { - publishDir = [ - path: { "${params.outdir}/metadata" }, - enabled: false - ] - } - - withName: SRA_RUNINFO_TO_FTP { - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SRA_FASTQ_FTP { - ext.args = '--retry 5 --continue-at - --max-time 1200' - publishDir = [ - [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ], - [ - path: { "${params.outdir}/fastq/md5" }, - mode: params.publish_dir_mode, - pattern: "*.md5" - ] - ] - } + withName: SRA_IDS_TO_RUNINFO { + publishDir = [ + path: { "${params.outdir}/metadata" }, + enabled: false + ] + } - withName: SRATOOLS_PREFETCH { - publishDir = [ - path: { "${params.outdir}/sra" }, - enabled: false - ] - } + withName: SRA_RUNINFO_TO_FTP { + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } - withName: SRATOOLS_FASTERQDUMP { - ext.args = '--split-files --include-technical' - publishDir = [ + withName: SRA_FASTQ_FTP { + ext.args = '--retry 5 --continue-at - --max-time 1200' + publishDir = [ + [ path: { "${params.outdir}/fastq" }, mode: params.publish_dir_mode, pattern: "*.fastq.gz" + ], + [ + path: { "${params.outdir}/fastq/md5" }, + mode: params.publish_dir_mode, + pattern: "*.md5" ] - } + ] + } - withName: SRA_TO_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - enabled: false - ] - } + withName: SRATOOLS_PREFETCH { + publishDir = [ + path: { "${params.outdir}/sra" }, + enabled: false + ] + } - withName: SRA_MERGE_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } + withName: SRATOOLS_FASTERQDUMP { + ext.args = '--split-files --include-technical' + publishDir = [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ] + } - withName: MULTIQC_MAPPINGS_CONFIG { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } + withName: SRA_TO_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + enabled: false + ] + } + + withName: SRA_MERGE_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: MULTIQC_MAPPINGS_CONFIG { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } } diff --git a/conf/modules/synapse.config b/conf/modules/synapse.config index bcca94db..2f52aa6f 100644 --- a/conf/modules/synapse.config +++ b/conf/modules/synapse.config @@ -13,57 +13,54 @@ // // Process options for the Synapse workflow // -if (params.input_type == 'synapse') { - process { +process { - withName: SYNAPSE_LIST { - ext.args = '--long' - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SYNAPSE_GET { - publishDir = [ - [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ], - [ - path: { "${params.outdir}/fastq/md5" }, - mode: params.publish_dir_mode, - pattern: "*.md5" - ] - ] - } + withName: SYNAPSE_LIST { + ext.args = '--long' + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } - withName: SYNAPSE_SHOW { - publishDir = [ - path: { "${params.outdir}/metadata" }, + withName: SYNAPSE_GET { + publishDir = [ + [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ], + [ + path: { "${params.outdir}/fastq/md5" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*.md5" ] - } + ] + } - withName: SYNAPSE_TO_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - enabled: false - ] - } + withName: SYNAPSE_SHOW { + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } - withName: SYNAPSE_MERGE_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } + withName: SYNAPSE_TO_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + enabled: false + ] + } + withName: SYNAPSE_MERGE_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } } From 464397c9225cccb293240cfefcf0fded5915a985 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 24 Aug 2023 15:07:04 +0100 Subject: [PATCH 009/175] Add emit statement to synpase workflow --- workflows/sra/main.nf | 8 +++++--- workflows/synapse/main.nf | 5 +++++ workflows/synapse/tests/main.nf.test.snap | 16 ++++++++++++++++ 3 files changed, 26 insertions(+), 3 deletions(-) create mode 100644 workflows/synapse/tests/main.nf.test.snap diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 3ca9b33e..e60386f9 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -168,9 +168,11 @@ workflow SRA { ) emit: - fastq = fastq_files - samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet - mapping = SRA_MERGE_SAMPLESHEET.out.mappings + fastq = fastq_files + samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet + mapping = SRA_MERGE_SAMPLESHEET.out.mappings + multiqc_config = MULTIQC_MAPPINGS_CONFIG.out.yml + versions = ch_versions.unique() } /* diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index f8cbeba1..0753a521 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -133,6 +133,11 @@ workflow SYNAPSE { CUSTOM_DUMPSOFTWAREVERSIONS ( ch_versions.unique().collectFile(name: 'collated_versions.yml') ) + + emit: + fastq = ch_fastq + samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet + versions = ch_versions.unique() } /* diff --git a/workflows/synapse/tests/main.nf.test.snap b/workflows/synapse/tests/main.nf.test.snap new file mode 100644 index 00000000..8528f776 --- /dev/null +++ b/workflows/synapse/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "samplesheet": { + "content": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", + "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548", + "samplesheet.csv:md5,9b3c35e8af74e9af194baa2498aaf4d4" + ], + "timestamp": "2023-08-24T14:05:07+0000" + }, + "software_versions": { + "content": [ + "software_versions.yml:md5,f37983a6b1ce2334fe62fa188b31ca51" + ], + "timestamp": "2023-08-24T14:05:07+0000" + } +} \ No newline at end of file From 97af5cd85d6c20127c16dee4b3f158867943bbbf Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 24 Aug 2023 15:53:28 +0100 Subject: [PATCH 010/175] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8573dea7..20dd21f8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Enhancements & fixes - [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests -- Emits all files in workflow for testing and enabling workflow to be imported when supported by Nextflow +- [#184](https://github.com/nf-core/fetchngs/pull/184/files) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow) ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16 From c7ab8b8bb2240d0d27a341e0ea20b4efec3f4913 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Aug 2023 18:07:07 +0200 Subject: [PATCH 011/175] move out multiqc and versions --- main.nf | 42 ++++++++++++++++++++++++++++++++++++ workflows/sra/main.nf | 45 +++++---------------------------------- workflows/synapse/main.nf | 15 ------------- 3 files changed, 47 insertions(+), 55 deletions(-) diff --git a/main.nf b/main.nf index 6da732be..e9bce9cd 100644 --- a/main.nf +++ b/main.nf @@ -31,6 +31,15 @@ Channel .unique() .set { ch_ids } +/* +======================================================================================== + IMPORT MODULES/SUBWORKFLOWS +======================================================================================== +*/ + +include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' +include { MULTIQC_MAPPINGS_CONFIG } from './modules/local/multiqc_mappings_config' + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOW FOR PIPELINE @@ -62,18 +71,37 @@ if (params.input_type == input_type) { // workflow NFCORE_FETCHNGS { + ch_versions = Channel.empty() + // // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids // if (params.input_type == 'sra') { SRA ( ch_ids ) + // + // MODULE: Create a MutiQC config file with sample name mappings + // + if (params.sample_mapping_fields) { + MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings) + ch_versions = SRA.out.versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) + } + + // + // MODULE: Dump software versions for all tools used in the workflow + // + // // WORKFLOW: Download FastQ files for Synapse ids // } else if (params.input_type == 'synapse') { SYNAPSE ( ch_ids ) + ch_versions = SYNAPSE.out.versions } + + CUSTOM_DUMPSOFTWAREVERSIONS ( + ch_versions.unique().collectFile(name: 'collated_versions.yml') + ) } /* @@ -90,6 +118,20 @@ workflow { NFCORE_FETCHNGS () } +/* +======================================================================================== + COMPLETION EMAIL AND SUMMARY +======================================================================================== +*/ + +workflow.onComplete { + if (params.email || params.email_on_fail) { + NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) + } + NfcoreTemplate.summary(workflow, params, log) + WorkflowSra.curateSamplesheetWarn(log) +} + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index e60386f9..d4612cd0 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -24,7 +24,6 @@ include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp' include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet' -include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config' /* ======================================================================================== @@ -32,8 +31,6 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions' - include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools' /* @@ -86,9 +83,9 @@ workflow SRA { if (!params.skip_fastq_download) { ch_sra_metadata - .map { - meta -> - [ meta, [ meta.fastq_1, meta.fastq_2 ] ] + .map { + meta -> + [ meta, [ meta.fastq_1, meta.fastq_2 ] ] } .branch { ftp: it[0].fastq_1 && !params.force_sratools_download @@ -120,7 +117,7 @@ workflow SRA { ) fastq_files - .map { + .map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() @@ -150,45 +147,13 @@ workflow SRA { ) ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) - // - // MODULE: Create a MutiQC config file with sample name mappings - // - if (params.sample_mapping_fields) { - MULTIQC_MAPPINGS_CONFIG ( - SRA_MERGE_SAMPLESHEET.out.mappings - ) - ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) - } - - // - // MODULE: Dump software versions for all tools used in the workflow - // - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) - emit: fastq = fastq_files samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet - mapping = SRA_MERGE_SAMPLESHEET.out.mappings - multiqc_config = MULTIQC_MAPPINGS_CONFIG.out.yml + mappings = SRA_MERGE_SAMPLESHEET.out.mappings versions = ch_versions.unique() } -/* -======================================================================================== - COMPLETION EMAIL AND SUMMARY -======================================================================================== -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) - } - NfcoreTemplate.summary(workflow, params, log) - WorkflowSra.curateSamplesheetWarn(log) -} - /* ======================================================================================== THE END diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 0753a521..34c3e315 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -25,14 +25,6 @@ include { SYNAPSE_GET } from '../../modules/local/synapse_get' include { SYNAPSE_TO_SAMPLESHEET } from '../../modules/local/synapse_to_samplesheet' include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet' -/* -======================================================================================== - IMPORT NF-CORE MODULES/SUBWORKFLOWS -======================================================================================== -*/ - -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions' - /* ======================================================================================== RUN MAIN WORKFLOW @@ -127,13 +119,6 @@ workflow SYNAPSE { ) ch_versions = ch_versions.mix(SYNAPSE_MERGE_SAMPLESHEET.out.versions) - // - // MODULE: Dump software versions for all tools used in the workflow - // - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) - emit: fastq = ch_fastq samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet From 372f9e434af68b1a854e8a68a8bec73510ca8ab9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Aug 2023 18:10:41 +0200 Subject: [PATCH 012/175] enable tests in refactor --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 451613fb..2a30309b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -4,10 +4,12 @@ on: push: branches: - dev + - refactor pull_request: branches: - dev - master + - refactor release: types: - "published" From 5dab8d0fa3e790ecb7baaced1fe08c9d01e994ec Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 24 Aug 2023 18:16:24 +0200 Subject: [PATCH 013/175] Apply suggestions from code review --- main.nf | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/main.nf b/main.nf index e9bce9cd..0f48d3c8 100644 --- a/main.nf +++ b/main.nf @@ -86,11 +86,6 @@ workflow NFCORE_FETCHNGS { MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings) ch_versions = SRA.out.versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) } - - // - // MODULE: Dump software versions for all tools used in the workflow - // - // // WORKFLOW: Download FastQ files for Synapse ids // @@ -99,6 +94,9 @@ workflow NFCORE_FETCHNGS { ch_versions = SYNAPSE.out.versions } + // + // MODULE: Dump software versions for all tools used in the workflow + // CUSTOM_DUMPSOFTWAREVERSIONS ( ch_versions.unique().collectFile(name: 'collated_versions.yml') ) From aff72b7ecc372162ba88759c2033fe601885c16d Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 24 Aug 2023 18:43:03 +0200 Subject: [PATCH 014/175] Apply suggestions from code review Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- main.nf | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index 0f48d3c8..2b852884 100644 --- a/main.nf +++ b/main.nf @@ -78,20 +78,25 @@ workflow NFCORE_FETCHNGS { // if (params.input_type == 'sra') { SRA ( ch_ids ) + ch_versions = ch_versions.mix(SRA.out.versions) + } // - // MODULE: Create a MutiQC config file with sample name mappings + // MODULE: Create a MultiQC config file with sample name mappings // if (params.sample_mapping_fields) { MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings) - ch_versions = SRA.out.versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) + ch_versions = ch_versions.mix( + SRA.out.versions, + MULTIQC_MAPPINGS_CONFIG.out.versions + ) } // // WORKFLOW: Download FastQ files for Synapse ids // } else if (params.input_type == 'synapse') { SYNAPSE ( ch_ids ) - ch_versions = SYNAPSE.out.versions + ch_versions = ch_versions.mix(SYNAPSE.out.versions) } // From 7f6439c1e6affd62bc13f76e63fd48ce6e262a75 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Aug 2023 18:46:00 +0200 Subject: [PATCH 015/175] fix syntax --- main.nf | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/main.nf b/main.nf index 2b852884..5311164f 100644 --- a/main.nf +++ b/main.nf @@ -79,17 +79,12 @@ workflow NFCORE_FETCHNGS { if (params.input_type == 'sra') { SRA ( ch_ids ) ch_versions = ch_versions.mix(SRA.out.versions) - } - // // MODULE: Create a MultiQC config file with sample name mappings // if (params.sample_mapping_fields) { MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings) - ch_versions = ch_versions.mix( - SRA.out.versions, - MULTIQC_MAPPINGS_CONFIG.out.versions - ) + ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) } // // WORKFLOW: Download FastQ files for Synapse ids From 6355a331d97c8f12815926901404760feed3238c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 10:36:33 +0200 Subject: [PATCH 016/175] small refactor --- main.nf | 65 ++++++++++++++++++--------------------- workflows/synapse/main.nf | 14 --------- 2 files changed, 30 insertions(+), 49 deletions(-) diff --git a/main.nf b/main.nf index 5311164f..edb54fd8 100644 --- a/main.nf +++ b/main.nf @@ -1,20 +1,20 @@ #!/usr/bin/env nextflow /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== nf-core/fetchngs -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== Github : https://github.com/nf-core/fetchngs Website: https://nf-co.re/fetchngs Slack : https://nfcore.slack.com/channels/fetchngs ----------------------------------------------------------------------------------------- +======================================================================================== */ nextflow.enable.dsl = 2 /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== VALIDATE & PRINT PARAMETER SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ WorkflowMain.initialise(workflow, params, log) @@ -24,16 +24,21 @@ ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) {exit 1, "File provided with --input is empty: ${ch_input.getName()}!"} // Read in ids from --input file -Channel - .from(file(params.input, checkIfExists: true)) +ch_ids = Channel.from(file(params.input, checkIfExists: true)) .splitCsv(header:false, sep:'', strip:true) .map { it[0] } .unique() - .set { ch_ids } + +// Auto-detect input type +def input_type = '' +if (WorkflowMain.isSraId(ch_input)) { input_type = 'sra' } +else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' } +else { exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!' } +if (params.input_type != input_type) { exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" } /* ======================================================================================== - IMPORT MODULES/SUBWORKFLOWS + IMPORT MODULES ======================================================================================== */ @@ -41,30 +46,19 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftw include { MULTIQC_MAPPINGS_CONFIG } from './modules/local/multiqc_mappings_config' /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOW FOR PIPELINE -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== + IMPORT WORKFLOWS +======================================================================================== */ -// Auto-detect input id type -def input_type = '' -if (WorkflowMain.isSraId(ch_input)) { - input_type = 'sra' -} else if (WorkflowMain.isSynapseId(ch_input)) { - input_type = 'synapse' -} else { - exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!' -} +if (params.input_type == 'sra') include { SRA } from './workflows/sra' +if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse' -if (params.input_type == input_type) { - if (params.input_type == 'sra') { - include { SRA } from './workflows/sra' - } else if (params.input_type == 'synapse') { - include { SYNAPSE } from './workflows/synapse' - } -} else { - exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" -} +/* +======================================================================================== + NAMED WORKFLOW FOR PIPELINE +======================================================================================== +*/ // // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided @@ -77,13 +71,13 @@ workflow NFCORE_FETCHNGS { // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids // if (params.input_type == 'sra') { - SRA ( ch_ids ) + SRA(ch_ids) ch_versions = ch_versions.mix(SRA.out.versions) // // MODULE: Create a MultiQC config file with sample name mappings // if (params.sample_mapping_fields) { - MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings) + MULTIQC_MAPPINGS_CONFIG(SRA.out.mappings) ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) } // @@ -127,11 +121,12 @@ workflow.onComplete { NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) } NfcoreTemplate.summary(workflow, params, log) - WorkflowSra.curateSamplesheetWarn(log) + if (params.input_type == 'sra') { WorkflowSra.curateSamplesheetWarn(log) } + if (params.input_type == 'synapse') { WorkflowSynapse.curateSamplesheetWarn(log) } } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== THE END -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 34c3e315..04bb32cb 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -125,20 +125,6 @@ workflow SYNAPSE { versions = ch_versions.unique() } -/* -======================================================================================== - COMPLETION EMAIL AND SUMMARY -======================================================================================== -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) - } - NfcoreTemplate.summary(workflow, params, log) - WorkflowSynapse.curateSamplesheetWarn(log) -} - /* ======================================================================================== THE END From ef03d06a9ec70aecc56d792a754bd900af0eb5d3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 10:46:38 +0200 Subject: [PATCH 017/175] staging --- workflows/sra/tests/main.nf.test | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 39a5cc3f..68ba7b58 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -1,7 +1,8 @@ -nextflow_pipeline { +nextflow_workflow { - name "Test workflow: sra.nf" - script "main.nf" + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" tag "workflows" tag "workflows_sra" tag "sra_default_parameters" From 1be5ebca09466fe99306fd638dccb9e529652324 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 10:51:52 +0200 Subject: [PATCH 018/175] validate input in main.nf --- main.nf | 32 +++++++++++++++++++++++++++++++- workflows/sra/main.nf | 15 --------------- workflows/synapse/main.nf | 18 ++---------------- 3 files changed, 33 insertions(+), 32 deletions(-) diff --git a/main.nf b/main.nf index edb54fd8..ef79d02b 100644 --- a/main.nf +++ b/main.nf @@ -36,6 +36,36 @@ else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' } else { exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!' } if (params.input_type != input_type) { exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" } +/* +======================================================================================== + VALIDATE INPUTS +======================================================================================== +*/ + +if (params.input_type == 'sra') { + def valid_params = [ + ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5'] + ] + + def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) + + // Validate input parameters + WorkflowSra.initialise(params, valid_params) +} + +if (params.input_type == 'synapse') { + + def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) + + // Create channel for synapse config + if (params.synapse_config) { + ch_synapse_config = file(params.synapse_config, checkIfExists: true) + } else { + exit 1, 'Please provide a Synapse config file for download authentication!' + } + +} + /* ======================================================================================== IMPORT MODULES @@ -84,7 +114,7 @@ workflow NFCORE_FETCHNGS { // WORKFLOW: Download FastQ files for Synapse ids // } else if (params.input_type == 'synapse') { - SYNAPSE ( ch_ids ) + SYNAPSE(ch_ids, ch_synapse_config) ch_versions = ch_versions.mix(SYNAPSE.out.versions) } diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index d4612cd0..d999d998 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -1,18 +1,3 @@ -/* -======================================================================================== - VALIDATE INPUTS -======================================================================================== -*/ - -def valid_params = [ - ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5'] -] - -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) - -// Validate input parameters -WorkflowSra.initialise(params, valid_params) - /* ======================================================================================== IMPORT LOCAL MODULES/SUBWORKFLOWS diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 04bb32cb..30d05f4f 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -1,18 +1,3 @@ -/* -======================================================================================== - VALIDATE INPUTS -======================================================================================== -*/ - -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) - -// Create channel for synapse config -if (params.synapse_config) { - ch_synapse_config = file(params.synapse_config, checkIfExists: true) -} else { - exit 1, 'Please provide a Synapse config file for download authentication!' -} - /* ======================================================================================== IMPORT LOCAL MODULES/SUBWORKFLOWS @@ -34,7 +19,8 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_sa workflow SYNAPSE { take: - ids // channel: [ ids ] + ids // channel: [ ids ] + ch_synapse_config // channel: [ synapse_config ] main: ch_versions = Channel.empty() From 698fab108f7638736768cb9a67140ce6801bd3ad Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 11:08:13 +0200 Subject: [PATCH 019/175] use error --- main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index ef79d02b..7575eeb8 100644 --- a/main.nf +++ b/main.nf @@ -21,7 +21,7 @@ WorkflowMain.initialise(workflow, params, log) // Check if --input file is empty ch_input = file(params.input, checkIfExists: true) -if (ch_input.isEmpty()) {exit 1, "File provided with --input is empty: ${ch_input.getName()}!"} +if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } // Read in ids from --input file ch_ids = Channel.from(file(params.input, checkIfExists: true)) @@ -33,8 +33,8 @@ ch_ids = Channel.from(file(params.input, checkIfExists: true)) def input_type = '' if (WorkflowMain.isSraId(ch_input)) { input_type = 'sra' } else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' } -else { exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!' } -if (params.input_type != input_type) { exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" } +else { error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') } +if (params.input_type != input_type) { error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") } /* ======================================================================================== @@ -61,7 +61,7 @@ if (params.input_type == 'synapse') { if (params.synapse_config) { ch_synapse_config = file(params.synapse_config, checkIfExists: true) } else { - exit 1, 'Please provide a Synapse config file for download authentication!' + error('Please provide a Synapse config file for download authentication!') } } From e83e909954168129e5f94ddae48493fff505c05d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 12:14:32 +0200 Subject: [PATCH 020/175] use workflow testing --- workflows/sra/tests/main.nf.test | 6 +- workflows/sra/tests/main.nf.test.snap | 80 +-------------------------- 2 files changed, 5 insertions(+), 81 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 68ba7b58..22ed6744 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -10,8 +10,10 @@ nextflow_workflow { test("Parameters: default") { when { - params { - outdir = "$outputDir" + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 88ea9654..3261e286 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -5,84 +5,6 @@ } ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:09:45+0000" + "timestamp": "2023-08-25T10:11:12+0000" } } \ No newline at end of file From 883a191ec257032a2714ce4683c742a719e33a66 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 13:27:52 +0200 Subject: [PATCH 021/175] update snapshot --- workflows/sra/tests/main.nf.test | 5 +- workflows/sra/tests/main.nf.test.snap | 1347 ++++++++++++++++++++++++- 2 files changed, 1349 insertions(+), 3 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 22ed6744..2652eb80 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -15,12 +15,15 @@ nextflow_workflow { input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') """ } + params { + outdir = "$outputDir" + } } then { assertAll( { assert workflow.success }, - { assert snapshot(process.out).match() } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 3261e286..a0cfc3f8 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -2,9 +2,1352 @@ "Parameters: default": { "content": [ { - + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": "GENOMIC", + "library_strategy": "OTHER", + "library_name": "IpeRAD1_3", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "base_count": "62550", + "read_count": "417", + "tax_id": "35883", + "scientific_name": "Ipomoea nil", + "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21", + "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098", + "study_title": "The Japanese morning glory genome sequence", + "sample_description": "Keywords: GSC:MIxS MIGS:6.0", + "fastq_md5": 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"fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_2": "", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "single_end": true + }, + "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83" + ] + ], + "mappings": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "samplesheet": [ + "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" + ], + "versions": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ] } ], - "timestamp": "2023-08-25T10:11:12+0000" + "timestamp": "2023-08-25T11:27:09+0000" } } \ No newline at end of file From da650afaf646bb4156b81ed0442d0764b7df802c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 14:22:05 +0200 Subject: [PATCH 022/175] restore versions --- modules.json | 3 +-- .../custom-dumpsoftwareversions.diff | 13 ------------- .../templates/dumpsoftwareversions.py | 1 + 3 files changed, 2 insertions(+), 15 deletions(-) delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff diff --git a/modules.json b/modules.json index 2244addd..3137b88b 100644 --- a/modules.json +++ b/modules.json @@ -8,8 +8,7 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"], - "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff" + "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { "branch": "master", diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff deleted file mode 100644 index a7893b24..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/custom/dumpsoftwareversions' ---- modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py -+++ modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py -@@ -75,7 +75,6 @@ - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { -- "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - -************************************************************ diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index 33d127f8..da033408 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -75,6 +75,7 @@ def main(): versions_by_module[module] = process_versions versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", "$workflow.manifest.name": "$workflow.manifest.version", } From f2d32d25153c9058e1641243849b06fd872316f1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 14:22:19 +0200 Subject: [PATCH 023/175] update workflow --- workflows/sra/main.nf | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index d999d998..44f6c6f5 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -49,18 +49,17 @@ workflow SRA { ) ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first()) - SRA_RUNINFO_TO_FTP + ch_sra_metadata = SRA_RUNINFO_TO_FTP .out .tsv .splitCsv(header:true, sep:'\t') - .map { - meta -> - def meta_clone = meta.clone() - meta_clone.single_end = meta_clone.single_end.toBoolean() - return meta_clone + .map{ meta -> + def meta_clone = meta.clone() + meta_clone.single_end = meta_clone.single_end.toBoolean() + return meta_clone } .unique() - .set { ch_sra_metadata } + ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first()) fastq_files = Channel.empty() @@ -101,16 +100,17 @@ workflow SRA { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads ) - fastq_files - .map { - meta, fastq -> - def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] - def meta_clone = meta.clone() - meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : '' - meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : '' - return meta_clone - } - .set { ch_sra_metadata } + ch_sra_metadata = fastq_files.map { meta, fastq -> + def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] + def meta_clone = meta.clone() + + meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : '' + meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : '' + + return meta_clone + } + + fastq_only_files = fastq_files.map { meta, fastq -> [fastq] } } // @@ -133,10 +133,10 @@ workflow SRA { ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) emit: - fastq = fastq_files - samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet - mappings = SRA_MERGE_SAMPLESHEET.out.mappings - versions = ch_versions.unique() + fastq = fastq_only_files + samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet + mappings = SRA_MERGE_SAMPLESHEET.out.mappings + versions = ch_versions.unique() } /* From 3018118620e39e313c4e9c9991981e128fff4bdc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 14:22:46 +0200 Subject: [PATCH 024/175] update snapshot --- workflows/sra/tests/main.nf.test.snap | 1282 ++----------------------- 1 file changed, 56 insertions(+), 1226 deletions(-) diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index a0cfc3f8..5d4aeaf2 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -4,661 +4,76 @@ { "0": [ [ - { - "id": "DRX024467_DRR026872", - "run_accession": "DRR026872", - "experiment_accession": "DRX024467", - "sample_accession": "SAMD00023098", - "secondary_sample_accession": "DRS033740", - "study_accession": "PRJDB4356", - "secondary_study_accession": "DRP003256", - "submission_accession": "DRA002758", - "run_alias": "DRR026872", - "experiment_alias": "DRX024467", - "sample_alias": "SAMD00023098", - "study_alias": "DRP003256", - "library_layout": "SINGLE", - "library_selection": "Restriction Digest", - "library_source": "GENOMIC", - "library_strategy": "OTHER", - "library_name": "IpeRAD1_3", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "62550", - "read_count": "417", - "tax_id": "35883", - "scientific_name": "Ipomoea nil", - "sample_title": "F2 plant dreived from a cross between Tokyo Kokei-standard and Africa #21", - "experiment_title": "Illumina HiSeq 2500 sequencing: Illumina HiSeq 2500 sequencing of SAMD00023098", - "study_title": "The Japanese morning glory genome sequence", - 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input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872') """ } params { diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 5d4aeaf2..0d94075c 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -3,181 +3,43 @@ "content": [ { "0": [ - [ - [ - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" - ] - ], - [ - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6" - ], - [ - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], - [ - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ], [ "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791" - ], - [ - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda" - ], - [ - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64" - ], - [ - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83" - ], - [ - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544" - ], - [ - [ - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2" - ] - ], - [ - [ - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76" - ] - ], - [ - [ - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88" - ] - ], - [ - [ - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962" - ] - ], - [ - [ - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04" - ] - ], - [ - [ - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79" - ] ] ], "1": [ - "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" + "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" ], "fastq": [ - [ - [ - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" - ] - ], - [ - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6" - ], - [ - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], - [ - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ], [ "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791" - ], - [ - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda" - ], - [ - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64" - ], - [ - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83" - ], - [ - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544" - ], - [ - [ - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2" - ] - ], - [ - [ - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76" - ] - ], - [ - [ - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88" - ] - ], - [ - [ - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962" - ] - ], - [ - [ - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04" - ] - ], - [ - [ - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79" - ] ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7" ], "samplesheet": [ - "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" + "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" ] } ], - "timestamp": "2023-08-25T12:20:20+0000" + "timestamp": "2023-08-25T12:56:07+0000" } -} +} \ No newline at end of file From f5d904030a96166699cef738438f17922afebbf3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 15:17:43 +0200 Subject: [PATCH 026/175] one emit statement at a time --- workflows/sra/main.nf | 3 --- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/main.nf.test.snap | 22 ++++++---------------- 3 files changed, 7 insertions(+), 20 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 44f6c6f5..8acb3da6 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -109,8 +109,6 @@ workflow SRA { return meta_clone } - - fastq_only_files = fastq_files.map { meta, fastq -> [fastq] } } // @@ -133,7 +131,6 @@ workflow SRA { ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) emit: - fastq = fastq_only_files samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet mappings = SRA_MERGE_SAMPLESHEET.out.mappings versions = ch_versions.unique() diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 6c4ecf17..2652eb80 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872') + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') """ } params { diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 0d94075c..a552d171 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -3,33 +3,23 @@ "content": [ { "0": [ - [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791" - ] + "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" ], "1": [ - "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646" + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "2": [ - "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7" - ], - "3": [ "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" ], - "fastq": [ - [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791" - ] - ], "mappings": [ - "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7" + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "samplesheet": [ - "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646" + "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" ], "versions": [ "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -40,6 +30,6 @@ ] } ], - "timestamp": "2023-08-25T12:56:07+0000" + "timestamp": "2023-08-25T13:15:46+0000" } -} \ No newline at end of file +} From ac35bc092fcbbf57e95abf1112567fb272ca2b12 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 16:47:43 +0200 Subject: [PATCH 027/175] polish --- main.nf | 16 +++-------- workflows/sra/main.nf | 3 ++- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/main.nf.test.snap | 38 ++++++--------------------- 4 files changed, 15 insertions(+), 44 deletions(-) diff --git a/main.nf b/main.nf index 7575eeb8..ad72ea4a 100644 --- a/main.nf +++ b/main.nf @@ -97,33 +97,25 @@ workflow NFCORE_FETCHNGS { ch_versions = Channel.empty() - // // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids - // if (params.input_type == 'sra') { SRA(ch_ids) ch_versions = ch_versions.mix(SRA.out.versions) - // - // MODULE: Create a MultiQC config file with sample name mappings - // + + // MODULE: Create a MultiQC config file with sample name mappings if (params.sample_mapping_fields) { MULTIQC_MAPPINGS_CONFIG(SRA.out.mappings) ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) } - // + // WORKFLOW: Download FastQ files for Synapse ids - // } else if (params.input_type == 'synapse') { SYNAPSE(ch_ids, ch_synapse_config) ch_versions = ch_versions.mix(SYNAPSE.out.versions) } - // // MODULE: Dump software versions for all tools used in the workflow - // - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml')) } /* diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 8acb3da6..c1583956 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -12,7 +12,7 @@ include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesh /* ======================================================================================== - IMPORT NF-CORE MODULES/SUBWORKFLOWS + IMPORT NF-CORE SUBWORKFLOWS ======================================================================================== */ @@ -131,6 +131,7 @@ workflow SRA { ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) emit: + fastq = fastq_files samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet mappings = SRA_MERGE_SAMPLESHEET.out.mappings versions = ch_versions.unique() diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 2652eb80..92b482bd 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -23,7 +23,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot(workflow.out.mappings, workflow.out.samplesheet).match() } ) } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index a552d171..8f577ef1 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -1,35 +1,13 @@ { "Parameters: default": { "content": [ - { - "0": [ - "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" - ], - "1": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" - ], - "2": [ - "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" - ], - "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" - ], - "samplesheet": [ - "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" - ], - "versions": [ - "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" - ] - } + [ + "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7" + ], + [ + "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646" + ] ], - "timestamp": "2023-08-25T13:15:46+0000" + "timestamp": "2023-08-25T14:23:33+0000" } -} +} \ No newline at end of file From 2efa57f90ccd4f42c5cb298e3c638493d2d03fb9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 25 Aug 2023 17:07:44 +0200 Subject: [PATCH 028/175] update snapshot --- workflows/sra/main.nf | 3 +- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/main.nf.test.snap | 1374 ++++++++++++++++++++++++- 3 files changed, 1369 insertions(+), 10 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index c1583956..8d5149d2 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -66,7 +66,7 @@ workflow SRA { if (!params.skip_fastq_download) { - ch_sra_metadata + ch_sra_reads = ch_sra_metadata .map { meta -> [ meta, [ meta.fastq_1, meta.fastq_2 ] ] @@ -75,7 +75,6 @@ workflow SRA { ftp: it[0].fastq_1 && !params.force_sratools_download sra: !it[0].fastq_1 || params.force_sratools_download } - .set { ch_sra_reads } // // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 92b482bd..2652eb80 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -23,7 +23,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out.mappings, workflow.out.samplesheet).match() } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 8f577ef1..3db02451 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -1,13 +1,1373 @@ { "Parameters: default": { "content": [ - [ - "id_mappings.csv:md5,71ebb4334e4a319a1a007370e36c98f7" - ], - [ - "samplesheet.csv:md5,0f35f9485a633d9c581903abd611b646" - ] + { + "stderr": [ + + ], + "errorReport": null, + "exitStatus": 0, + "out": { + "0": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "secondary_sample_accession": "ERS951016", + "study_accession": "PRJEB11633", + "secondary_study_accession": "ERP013030", + "submission_accession": "ERA528939", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "library_selection": "RT-PCR", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "library_name": "unspecified", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "base_count": "29700", + "read_count": "169", + "tax_id": "63433", + "scientific_name": "Leptopilina boulardi", + "sample_title": "RNA-Seq reads mapped onto L. 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"library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "library_name": "GSM6601461", + "instrument_model": "Illumina HiSeq 4000", + "instrument_platform": "ILLUMINA", + "base_count": "677912850", + "read_count": "13558257", + "tax_id": "6239", + "scientific_name": "Caenorhabditis elegans", + "sample_title": "PM2.5-treated worms in day 5", + "experiment_title": "Illumina HiSeq 4000 sequencing: GSM6601461: PM2.5-treated worms in day 5 Caenorhabditis elegans RNA-Seq", + "study_title": "PM2.5 exposure induces lifespan reduction in Caenorhabditis elegans", + "sample_description": "PM2.5-treated worms in day 5", + "fastq_md5": "cbe4e9f967a71593f9ec3c6edaf11c83", + "fastq_bytes": "529798447", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21711855/SRR21711855.fastq.gz", + "fastq_2": "", + "md5_1": "cbe4e9f967a71593f9ec3c6edaf11c83", + "md5_2": "", + "single_end": true + }, + "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83" ] - }, - "failed": false, - "stdout": [ - "WARN: There's no process matching config selector: CUSTOM_DUMPSOFTWAREVERSIONS", - "WARN: There's no process matching config selector: MULTIQC_MAPPINGS_CONFIG" ], - "errorMessage": null, - "trace": { - "tasksFailed": 0, - "tasksCount": 57, - "tasksSucceeded": 57 - }, - "name": "workflow", - "success": true + "mappings": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "samplesheet": [ + "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" + ], + "versions": [ + "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ] } ], - "timestamp": "2023-08-25T15:06:56+0000" + "timestamp": "2023-08-25T15:13:41+0000" } } \ No newline at end of file From e8258ba4d77dae0e963c63558099c781f36c2435 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 11:17:16 +0200 Subject: [PATCH 031/175] order --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index ad72ea4a..0535bb57 100644 --- a/main.nf +++ b/main.nf @@ -72,8 +72,8 @@ if (params.input_type == 'synapse') { ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' include { MULTIQC_MAPPINGS_CONFIG } from './modules/local/multiqc_mappings_config' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' /* ======================================================================================== From f8322343c09fd45f30c503002d6542f1459f5d67 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 11:17:32 +0200 Subject: [PATCH 032/175] update test and snapshots --- workflows/sra/tests/main.nf.test | 7 +- workflows/sra/tests/main.nf.test.snap | 1043 ++++++++++++++----------- 2 files changed, 571 insertions(+), 479 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 2652eb80..4822da3d 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -23,7 +23,12 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } +// { assert snapshot(workflow.out).match() } + { assert new File("$outputDir/custom").exists() }, + { assert new File("$outputDir/metadata").exists() }, + { assert new File("$outputDir/pipeline_info").exists() }, + { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, + { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") } ) } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 3eab5807..62d0d976 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -45,6 +45,48 @@ }, "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791" ], + [ + { + "id": "SRX6725035_SRR9984183", + "run_accession": "SRR9984183", + "experiment_accession": "SRX6725035", + "sample_accession": "SAMN12581720", + "secondary_sample_accession": "SRS5277011", + "study_accession": "PRJNA560329", + "secondary_study_accession": "SRP218535", + "submission_accession": "SRA942061", + "run_alias": "Emb289P1_bin131.fastq", + "experiment_alias": "Emb289P1_bin131", + "sample_alias": "Emb289P1_bin131", + "study_alias": "PRJNA560329", + "library_layout": "SINGLE", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "library_name": "Emb289P1_bin131", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "base_count": "1996273", + "read_count": "58", + "tax_id": "2660712", + "scientific_name": "Defluviitaleaceae bacterium", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_2": "", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "single_end": true + }, + "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544" + ], [ { "id": "ERX1234253_ERR1160846", @@ -89,47 +131,47 @@ ], [ { - "id": "DRX026011_DRR028935", - "run_accession": "DRR028935", - "experiment_accession": "DRX026011", - "sample_accession": "SAMD00024405", - "secondary_sample_accession": "DRS019431", - "study_accession": "PRJDB3420", - "secondary_study_accession": "DRP002616", - "submission_accession": "DRA002949", - "run_alias": "DRR028935", - "experiment_alias": "DRX026011", - "sample_alias": "SAMD00024405", - "study_alias": "DRP002616", + "id": "SRX9626017_SRR13191702", + "run_accession": "SRR13191702", + "experiment_accession": "SRX9626017", + "sample_accession": "SAMN16980141", + "secondary_sample_accession": "SRS7827211", + "study_accession": "PRJNA682076", + "secondary_study_accession": "SRP295653", + "submission_accession": "SRA1166126", + "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz", + "experiment_alias": "S.170804.00784", + "sample_alias": "S.170804.00784_662", + "study_alias": "PRJNA682076", "library_layout": "PAIRED", - "library_selection": "cDNA", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "day0_BbSQE-I", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "library_name": "S.170804.00784", "instrument_model": "Illumina HiSeq 2500", "instrument_platform": "ILLUMINA", - "base_count": "194930", - "read_count": "965", - "tax_id": "1202541", - "scientific_name": "Botryococcus braunii Showa", - "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", - "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", - "sample_description": "Liquid culture", - "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", - "fastq_bytes": "60275;61610", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz", - "fastq_2": 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"fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz", + "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98", "single_end": false }, [ - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" ] ], [ @@ -179,105 +221,60 @@ ], [ { - "id": 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"DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", + "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", + "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", + "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", + "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", + "GSM4907283.runinfo_ftp.tsv:md5,090f3594af6ef6f5af4d9e4aaf030d18", + "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", + "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", + "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", + "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", + "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" + ], + "timestamp": "2023-08-28T08:57:15+0000" + }, + "samplesheet": { + "content": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", + "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" + ], + "timestamp": "2023-08-28T08:57:15+0000" + }, + "custom": { + "content": [ + "user-settings.mkfg:md5,a182ee157fbd89040a00b9658f53848d" + ], + "timestamp": "2023-08-28T08:57:15+0000" + }, + "fastq": { + "content": [ + "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", + "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", + "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", + "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", + "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", + "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", + "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", + "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", + "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", + "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", + "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", + "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", + "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", + "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", + "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", + "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", + "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", + "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", + "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", + "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", + "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", + [ + "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", + "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", + "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", + "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", + "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", + "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", + "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", + "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", + "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", + "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", + "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", + "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", + "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", + "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", + "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", + "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", + "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ], + "timestamp": "2023-08-28T08:57:15+0000" + }, + "pipeline_info": { + "content": [ + "execution_report_2023-08-28_10-54-32.html:md5,710a38308b41b4bd86b6d2d8fd4a72b7", + "execution_timeline_2023-08-28_10-54-32.html:md5,1583b3c97bc7c97a8550c3d0ce6302c8", + "pipeline_dag_2023-08-28_10-54-32.html:md5,63f58c7a48a1b71d3ee7809cb6a92740" + ], + "timestamp": "2023-08-28T08:57:15+0000" } -} \ No newline at end of file +} From 80892b7ca38100a00b31b5abb2c079694e2729a0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 13:06:34 +0200 Subject: [PATCH 033/175] update test --- workflows/sra/tests/main.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 4822da3d..2a1e82a1 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -27,8 +27,8 @@ nextflow_workflow { { assert new File("$outputDir/custom").exists() }, { assert new File("$outputDir/metadata").exists() }, { assert new File("$outputDir/pipeline_info").exists() }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") } + { assert new File("$outputDir/samplesheet").exists() }, + { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } ) } } From 9a70ce9bca6179b6d43f9bb2bb6326de8aa48343 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 14:27:56 +0200 Subject: [PATCH 034/175] update tests and snapshot --- .../sra_custom_ena_metadata_fields.nf.test | 19 +++++++++++++++---- ...ra_custom_ena_metadata_fields.nf.test.snap | 12 ++++++------ .../tests/sra_force_sratools_download.nf.test | 19 +++++++++++++++---- .../sra_nf_core_pipeline_atacseq.nf.test | 19 +++++++++++++++---- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 12 ++++++------ .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 19 +++++++++++++++---- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 12 ++++++------ .../sra_nf_core_pipeline_taxprofiler.nf.test | 19 +++++++++++++++---- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 12 ++++++------ .../sra_nf_core_pipeline_viralrecon.nf.test | 19 +++++++++++++++---- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 12 ++++++------ 11 files changed, 120 insertions(+), 54 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 6e27c4a9..f1f55f02 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -1,7 +1,8 @@ -nextflow_pipeline { +nextflow_workflow { - name "Test workflow: sra.nf" - script "main.nf" + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" tag "workflows" tag "workflows_sra" tag "sra_custom_ena_metadata_fields" @@ -9,6 +10,11 @@ nextflow_pipeline { test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } params { outdir = "$outputDir" nf_core_pipeline = "rnaseq" @@ -20,7 +26,12 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(process.out).match() } +// { assert snapshot(workflow.out).match() } + { assert new File("$outputDir/custom").exists() }, + { assert new File("$outputDir/metadata").exists() }, + { assert new File("$outputDir/pipeline_info").exists() }, + { assert new File("$outputDir/samplesheet").exists() }, + { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } ) } } diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 55c39d4f..ddd8e845 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -12,20 +12,20 @@ "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1", "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236" ], - "timestamp": "2023-08-17T12:11:42+0000" + "timestamp": "2023-08-28T09:29:59+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f", - "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040" + "samplesheet.csv:md5,7bca96e409bd9eb6790e0d6737af686c" ], - "timestamp": "2023-08-17T12:11:42+0000" + "timestamp": "2023-08-28T09:29:59+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-17T12:11:42+0000" + "timestamp": "2023-08-28T09:29:59+0000" }, "Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": { "content": [ @@ -33,7 +33,7 @@ } ], - "timestamp": "2023-08-17T12:11:42+0000" + "timestamp": "2023-08-28T09:29:59+0000" }, "fastq": { "content": [ @@ -83,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-17T12:11:42+0000" + "timestamp": "2023-08-28T09:29:59+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 1b501975..051e4aa5 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -1,7 +1,8 @@ -nextflow_pipeline { +nextflow_workflow { - name "Test workflow: sra.nf" - script "main.nf" + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" tag "workflows" tag "workflows_sra" tag "sra_force_sratools_download" @@ -9,6 +10,11 @@ nextflow_pipeline { test("Parameters: --force_sratools_download") { when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } params { outdir = "$outputDir" force_sratools_download = true @@ -18,7 +24,12 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(process.out).match() } +// { assert snapshot(workflow.out).match() } + { assert new File("$outputDir/custom").exists() }, + { assert new File("$outputDir/metadata").exists() }, + { assert new File("$outputDir/pipeline_info").exists() }, + { assert new File("$outputDir/samplesheet").exists() }, + { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index bda1d724..6925b971 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -1,7 +1,8 @@ -nextflow_pipeline { +nextflow_workflow { - name "Test workflow: sra.nf" - script "main.nf" + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" tag "workflows" tag "workflows_sra" tag "sra_nf_core_pipeline_atacseq" @@ -9,6 +10,11 @@ nextflow_pipeline { test("Parameters: --nf_core_pipeline atacseq") { when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } params { outdir = "$outputDir" nf_core_pipeline = "atacseq" @@ -18,7 +24,12 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(process.out).match() } +// { assert snapshot(workflow.out).match() } + { assert new File("$outputDir/custom").exists() }, + { assert new File("$outputDir/metadata").exists() }, + { assert new File("$outputDir/pipeline_info").exists() }, + { assert new File("$outputDir/samplesheet").exists() }, + { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index c99f258e..0ccec99b 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -12,20 +12,20 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-17T12:21:36+0000" + "timestamp": "2023-08-28T10:05:53+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" + "samplesheet.csv:md5,252449b9f66687af076bb5a9dfea4551" ], - "timestamp": "2023-08-17T12:21:36+0000" + "timestamp": "2023-08-28T10:05:53+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-17T12:21:36+0000" + "timestamp": "2023-08-28T10:05:53+0000" }, "Parameters: '--nf_core_pipeline atacseq'": { "content": [ @@ -33,7 +33,7 @@ } ], - "timestamp": "2023-08-17T12:21:36+0000" + "timestamp": "2023-08-28T10:05:53+0000" }, "fastq": { "content": [ @@ -83,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-17T12:21:36+0000" + "timestamp": "2023-08-28T10:05:57+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 438b7f55..a84b7c41 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -1,7 +1,8 @@ -nextflow_pipeline { +nextflow_workflow { - name "Test workflow: sra.nf" - script "main.nf" + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" tag "workflows" tag "workflows_sra" tag "sra_nf_core_pipeline_rnaseq" @@ -9,6 +10,11 @@ nextflow_pipeline { test("Parameters: --nf_core_pipeline rnaseq") { when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } params { outdir = "$outputDir" nf_core_pipeline = "rnaseq" @@ -18,7 +24,12 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(process.out).match() } +// { assert snapshot(workflow.out).match() } + { assert new File("$outputDir/custom").exists() }, + { assert new File("$outputDir/metadata").exists() }, + { assert new File("$outputDir/pipeline_info").exists() }, + { assert new File("$outputDir/samplesheet").exists() }, + { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 1da0381a..af68569e 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -12,20 +12,20 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-17T12:19:51+0000" + "timestamp": "2023-08-28T09:32:33+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" + "samplesheet.csv:md5,f0b7e9436c6feb1a31c49c2c8ab761a2" ], - "timestamp": "2023-08-17T12:19:51+0000" + "timestamp": "2023-08-28T09:32:33+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-17T12:19:51+0000" + "timestamp": "2023-08-28T09:32:33+0000" }, "Parameters: '--nf_core_pipeline rnaseq'": { "content": [ @@ -33,7 +33,7 @@ } ], - "timestamp": "2023-08-17T12:19:51+0000" + "timestamp": "2023-08-28T09:32:33+0000" }, "fastq": { "content": [ @@ -83,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-17T12:19:51+0000" + "timestamp": "2023-08-28T09:32:33+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 301938c4..c2022ce2 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -1,7 +1,8 @@ -nextflow_pipeline { +nextflow_workflow { - name "Test workflow: sra.nf" - script "main.nf" + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" tag "workflows" tag "workflows_sra" tag "sra_nf_core_pipeline_taxprofiler" @@ -9,6 +10,11 @@ nextflow_pipeline { test("Parameters: --nf_core_pipeline taxprofiler") { when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } params { outdir = "$outputDir" nf_core_pipeline = "taxprofiler" @@ -18,7 +24,12 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(process.out).match() } +// { assert snapshot(workflow.out).match() } + { assert new File("$outputDir/custom").exists() }, + { assert new File("$outputDir/metadata").exists() }, + { assert new File("$outputDir/pipeline_info").exists() }, + { assert new File("$outputDir/samplesheet").exists() }, + { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index 85f3957b..da686d45 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -12,20 +12,20 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-17T12:24:34+0000" + "timestamp": "2023-08-28T09:27:41+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" + "samplesheet.csv:md5,484efbb550b50f5ac63e4864282edea7" ], - "timestamp": "2023-08-17T12:24:34+0000" + "timestamp": "2023-08-28T09:27:41+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-17T12:24:34+0000" + "timestamp": "2023-08-28T09:27:41+0000" }, "Parameters: --nf_core_pipeline taxprofiler": { "content": [ @@ -33,7 +33,7 @@ } ], - "timestamp": "2023-08-17T12:24:34+0000" + "timestamp": "2023-08-28T09:27:41+0000" }, "fastq": { "content": [ @@ -83,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-17T12:24:34+0000" + "timestamp": "2023-08-28T09:27:41+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 892a7c3a..e664f0fd 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -1,7 +1,8 @@ -nextflow_pipeline { +nextflow_workflow { - name "Test workflow: sra.nf" - script "main.nf" + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" tag "workflows" tag "workflows_sra" tag "sra_nf_core_pipeline_viralrecon" @@ -9,6 +10,11 @@ nextflow_pipeline { test("Parameters: --nf_core_pipeline viralrecon") { when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } params { outdir = "$outputDir" nf_core_pipeline = "viralrecon" @@ -18,7 +24,12 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(process.out).match() } +// { assert snapshot(workflow.out).match() } + { assert new File("$outputDir/custom").exists() }, + { assert new File("$outputDir/metadata").exists() }, + { assert new File("$outputDir/pipeline_info").exists() }, + { assert new File("$outputDir/samplesheet").exists() }, + { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 13c59b5d..a30d8377 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -12,14 +12,14 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-17T12:26:57+0000" + "timestamp": "2023-08-28T10:03:01+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" + "samplesheet.csv:md5,3e32e2cfa3c8b23c9cd32d91b885c0de" ], - "timestamp": "2023-08-17T12:26:57+0000" + "timestamp": "2023-08-28T10:03:01+0000" }, "Parameters: --nf_core_pipeline viralrecon": { "content": [ @@ -27,13 +27,13 @@ } ], - "timestamp": "2023-08-17T12:26:57+0000" + "timestamp": "2023-08-28T10:03:01+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-17T12:26:57+0000" + "timestamp": "2023-08-28T10:03:01+0000" }, "fastq": { "content": [ @@ -83,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-17T12:26:57+0000" + "timestamp": "2023-08-28T10:03:06+0000" } } \ No newline at end of file From f1c9f4792a212f5d323e4dfd2897ac14ef18da71 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 14:36:24 +0200 Subject: [PATCH 035/175] update snapshot --- .../sra_force_sratools_download.nf.test.snap | 38 +------------------ 1 file changed, 1 insertion(+), 37 deletions(-) diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index d5d694da..331943c5 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -1,40 +1,4 @@ { - "Parameters: '--force_sratools_download'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, "fastq": { "content": [ "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85", @@ -62,6 +26,6 @@ "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7", "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af" ], - "timestamp": "2023-08-17T12:15:55+0000" + "timestamp": "2023-08-28T12:35:42+0000" } } \ No newline at end of file From eedee488a9dfaaa1fe43dd60f8647f2152c239ae Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 14:48:35 +0200 Subject: [PATCH 036/175] update test --- .../sra/tests/sra_skip_fastq_download.nf.test | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 7d218cf7..7180fd6d 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -1,7 +1,8 @@ -nextflow_pipeline { +nextflow_workflow { - name "Test workflow: sra.nf" - script "main.nf" + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" tag "workflows" tag "workflows_sra" tag "sra_skip_fastq_download" @@ -9,6 +10,11 @@ nextflow_pipeline { test("Parameters: --skip_fastq_download") { when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } params { outdir = "$outputDir" skip_fastq_download = true @@ -18,7 +24,10 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(process.out).match() } +// { assert snapshot(workflow.out).match() } + { assert new File("$outputDir/metadata").exists() }, + { assert new File("$outputDir/pipeline_info").exists() }, + { assert new File("$outputDir/samplesheet").exists() } ) } } From db29566dfc71ff5b24d390bb54dfc1fbdce65baf Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 14:51:45 +0200 Subject: [PATCH 037/175] need to update snapshot --- .../sra_skip_fastq_download.nf.test.snap | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap deleted file mode 100644 index d004d5d2..00000000 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ /dev/null @@ -1,46 +0,0 @@ -{ - "Parameters: '--skip_fastq_download'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "Parameters: --skip_fastq_download": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:25:19+0000" - } -} \ No newline at end of file From 57d7ba319a639bc33756df1ff2e8c229cf5b819a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 15:37:19 +0200 Subject: [PATCH 038/175] add nextflow.log to test output when failures --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2a30309b..d652f33e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -81,6 +81,7 @@ jobs: run: | sudo apt install bat > /dev/null batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml + batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log - name: Publish Test Report uses: mikepenz/action-junit-report@v3 From 57bf16705bf23fe2c7695774e2376f2c709a4d35 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 28 Aug 2023 15:43:35 +0200 Subject: [PATCH 039/175] add nextflow.log to test output when failures --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d652f33e..aa4b4cf9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -80,7 +80,6 @@ jobs: if: failure() run: | sudo apt install bat > /dev/null - batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log - name: Publish Test Report From 43223db40d2c1e26d14763bcd60ce5509adea749 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Sep 2023 15:49:53 +0200 Subject: [PATCH 040/175] test rc --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index aa4b4cf9..5c5df959 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,7 +16,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.7.3" + NFTEST_VER: "0.8.0-rc1" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From b40fe58f06b8f4909754eedddd5864bc614822b7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Sep 2023 15:50:42 +0200 Subject: [PATCH 041/175] re-able autoSort --- nf-test.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/nf-test.config b/nf-test.config index 217a5138..0799cb40 100644 --- a/nf-test.config +++ b/nf-test.config @@ -13,7 +13,4 @@ config { // run all test with the defined docker profile from the main nextflow.config profile "" - - // Disable autosort Channels - autoSort false } From d9168a159281225cbb01336c355b0ede6a752486 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Sep 2023 15:51:21 +0200 Subject: [PATCH 042/175] add .nf-test.log to gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 935326a7..b1b5890a 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ testing* *.pyc .nf-test/ nf-test +.nf-test.log From 359462f90f28ea91885685774c9c9d3d0d2870f6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Sep 2023 16:49:57 +0200 Subject: [PATCH 043/175] simplify tests --- workflows/sra/tests/main.nf.test | 7 +------ workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 7 +------ workflows/sra/tests/sra_force_sratools_download.nf.test | 7 +------ workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 7 +------ workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 7 +------ .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 7 +------ .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 7 +------ workflows/sra/tests/sra_skip_fastq_download.nf.test | 5 +---- 8 files changed, 8 insertions(+), 46 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 2a1e82a1..2652eb80 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -23,12 +23,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, -// { assert snapshot(workflow.out).match() } - { assert new File("$outputDir/custom").exists() }, - { assert new File("$outputDir/metadata").exists() }, - { assert new File("$outputDir/pipeline_info").exists() }, - { assert new File("$outputDir/samplesheet").exists() }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index f1f55f02..4dc9ba8b 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -26,12 +26,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, -// { assert snapshot(workflow.out).match() } - { assert new File("$outputDir/custom").exists() }, - { assert new File("$outputDir/metadata").exists() }, - { assert new File("$outputDir/pipeline_info").exists() }, - { assert new File("$outputDir/samplesheet").exists() }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 051e4aa5..2b1b5953 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -24,12 +24,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, -// { assert snapshot(workflow.out).match() } - { assert new File("$outputDir/custom").exists() }, - { assert new File("$outputDir/metadata").exists() }, - { assert new File("$outputDir/pipeline_info").exists() }, - { assert new File("$outputDir/samplesheet").exists() }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 6925b971..3d946fea 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -24,12 +24,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, -// { assert snapshot(workflow.out).match() } - { assert new File("$outputDir/custom").exists() }, - { assert new File("$outputDir/metadata").exists() }, - { assert new File("$outputDir/pipeline_info").exists() }, - { assert new File("$outputDir/samplesheet").exists() }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index a84b7c41..f51aa4ca 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -24,12 +24,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, -// { assert snapshot(workflow.out).match() } - { assert new File("$outputDir/custom").exists() }, - { assert new File("$outputDir/metadata").exists() }, - { assert new File("$outputDir/pipeline_info").exists() }, - { assert new File("$outputDir/samplesheet").exists() }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index c2022ce2..97cd4a44 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -24,12 +24,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, -// { assert snapshot(workflow.out).match() } - { assert new File("$outputDir/custom").exists() }, - { assert new File("$outputDir/metadata").exists() }, - { assert new File("$outputDir/pipeline_info").exists() }, - { assert new File("$outputDir/samplesheet").exists() }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index e664f0fd..434fac63 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -24,12 +24,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, -// { assert snapshot(workflow.out).match() } - { assert new File("$outputDir/custom").exists() }, - { assert new File("$outputDir/metadata").exists() }, - { assert new File("$outputDir/pipeline_info").exists() }, - { assert new File("$outputDir/samplesheet").exists() }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") } + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 7180fd6d..dbe40144 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -24,10 +24,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, -// { assert snapshot(workflow.out).match() } - { assert new File("$outputDir/metadata").exists() }, - { assert new File("$outputDir/pipeline_info").exists() }, - { assert new File("$outputDir/samplesheet").exists() } + { assert snapshot(workflow.out).match() } ) } } From b180a636ff039c69cf3bd79060ba8a5a98692fad Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Sep 2023 17:30:07 +0200 Subject: [PATCH 044/175] update snapshot --- workflows/sra/tests/main.nf.test.snap | 1707 ++++++++--------- ...ra_custom_ena_metadata_fields.nf.test.snap | 647 ++++++- .../sra_force_sratools_download.nf.test.snap | 1372 ++++++++++++- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 1427 +++++++++++++- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 1427 +++++++++++++- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 1425 +++++++++++++- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 1425 +++++++++++++- .../sra_skip_fastq_download.nf.test.snap | 37 + 8 files changed, 8141 insertions(+), 1326 deletions(-) create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 62d0d976..1c969bc2 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -47,131 +47,47 @@ ], [ { - "id": "SRX6725035_SRR9984183", - "run_accession": "SRR9984183", - "experiment_accession": "SRX6725035", - "sample_accession": "SAMN12581720", - "secondary_sample_accession": "SRS5277011", - "study_accession": "PRJNA560329", - "secondary_study_accession": "SRP218535", - "submission_accession": "SRA942061", - "run_alias": "Emb289P1_bin131.fastq", - "experiment_alias": "Emb289P1_bin131", - "sample_alias": "Emb289P1_bin131", - "study_alias": "PRJNA560329", - "library_layout": "SINGLE", - "library_selection": "RANDOM", - "library_source": "METAGENOMIC", - "library_strategy": "WGS", - "library_name": "Emb289P1_bin131", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "1996273", - "read_count": "58", - "tax_id": "2660712", - "scientific_name": "Defluviitaleaceae bacterium", - "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", - "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", - "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", - "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", - "fastq_md5": "0b512d2dc31685983456bd56fd836544", - "fastq_bytes": "605358", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", - "fastq_2": "", - "md5_1": "0b512d2dc31685983456bd56fd836544", - "md5_2": "", - "single_end": true - }, - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544" - ], - [ - { - "id": "ERX1234253_ERR1160846", - "run_accession": "ERR1160846", - "experiment_accession": "ERX1234253", - "sample_accession": "SAMEA3687214", - "secondary_sample_accession": "ERS994363", - "study_accession": "PRJEB11419", - "secondary_study_accession": "ERP012803", - "submission_accession": "ERA541392", - "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", - "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", - "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", - "study_alias": "qiita_sid_10317", - "library_layout": "SINGLE", - "library_selection": "PCR", - "library_source": "METAGENOMIC", - "library_strategy": "AMPLICON", - "library_name": "10317.BLANK.93.3E.r22", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "35658", - "read_count": "283", - "tax_id": "256318", - "scientific_name": "metagenome", - "sample_title": "10317.BLANK.93.3E.r22", - "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", - "study_title": "American Gut Project", - "sample_description": "American Gut control", - "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", - "fastq_bytes": "18077", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", - "fastq_2": "", - "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", - "md5_2": "", - "single_end": true - }, - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6" - ], - [ - { - "id": "SRX9626017_SRR13191702", - "run_accession": "SRR13191702", - "experiment_accession": "SRX9626017", - "sample_accession": "SAMN16980141", - "secondary_sample_accession": "SRS7827211", - "study_accession": "PRJNA682076", - "secondary_study_accession": "SRP295653", - "submission_accession": "SRA1166126", - "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz", - "experiment_alias": "S.170804.00784", - "sample_alias": "S.170804.00784_662", - "study_alias": "PRJNA682076", + "id": "DRX026011_DRR028935", + "run_accession": "DRR028935", + "experiment_accession": "DRX026011", + "sample_accession": "SAMD00024405", + "secondary_sample_accession": "DRS019431", + "study_accession": "PRJDB3420", + "secondary_study_accession": "DRP002616", + "submission_accession": "DRA002949", + "run_alias": "DRR028935", + "experiment_alias": "DRX026011", + "sample_alias": "SAMD00024405", + "study_alias": "DRP002616", "library_layout": "PAIRED", - "library_selection": "PCR", - "library_source": "METAGENOMIC", - "library_strategy": "AMPLICON", - "library_name": "S.170804.00784", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "library_name": "day0_BbSQE-I", "instrument_model": "Illumina HiSeq 2500", "instrument_platform": "ILLUMINA", - "base_count": "45682", - "read_count": "91", - "tax_id": "408170", - "scientific_name": "human gut metagenome", - "sample_title": "Metagenome or environmental sample from human gut metagenome", - "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", - "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", - "sample_description": "Metagenome or environmental sample from human gut metagenome", - "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98", - "fastq_bytes": "15420;16324", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz", - "fastq_2": 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"2023-08-28T10:03:06+0000" + "timestamp": "2023-09-11T16:33:01.320808" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap new file mode 100644 index 00000000..921bed59 --- /dev/null +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -0,0 +1,37 @@ +{ + "Parameters: --skip_fastq_download": { + "content": [ + { + "0": [ + + ], + "1": [ + "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + ], + "2": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "3": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ], + "fastq": [ + + ], + "mappings": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "samplesheet": [ + "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + ], + "versions": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ] + } + ], + "timestamp": "2023-09-11T16:58:42.10055" + } +} \ No newline at end of file From 07be381748947cf5d6c8d1d85be47c61c6735f52 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Sep 2023 17:30:23 +0200 Subject: [PATCH 045/175] update snapshot --- workflows/synapse/tests/main.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/synapse/tests/main.nf.test.snap b/workflows/synapse/tests/main.nf.test.snap index 8528f776..9b25ee0c 100644 --- a/workflows/synapse/tests/main.nf.test.snap +++ b/workflows/synapse/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548", - "samplesheet.csv:md5,9b3c35e8af74e9af194baa2498aaf4d4" + "samplesheet.csv:md5,296e139d533c7a67567dd073ec0f945a" ], - "timestamp": "2023-08-24T14:05:07+0000" + "timestamp": "2023-09-11T17:08:51.001588" }, "software_versions": { "content": [ - "software_versions.yml:md5,f37983a6b1ce2334fe62fa188b31ca51" + "software_versions.yml:md5,966251d4b7717464ccea77d6e8841e58" ], - "timestamp": "2023-08-24T14:05:07+0000" + "timestamp": "2023-09-11T17:08:50.994607" } } \ No newline at end of file From cedcf471f8c39d7f66c589fa36c1919ffe025ad1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Sep 2023 18:26:47 +0200 Subject: [PATCH 046/175] relative path --- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/main.nf.test.snap | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 2652eb80..ef35c80a 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 1c969bc2..1692d4cd 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -662,7 +662,7 @@ ] ], "1": [ - "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" + "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" ], "2": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" @@ -1337,7 +1337,7 @@ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "samplesheet": [ - "samplesheet.csv:md5,dbd0e9c1683c603c681184a13f5b7341" + "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" ], "versions": [ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", @@ -1348,6 +1348,6 @@ ] } ], - "timestamp": "2023-09-11T16:58:15.05829" + "timestamp": "2023-09-11T18:23:09.598326" } } \ No newline at end of file From b26115d7e453393355ca7d5638fcd0ed40f583eb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 11 Sep 2023 19:35:04 +0200 Subject: [PATCH 047/175] update tests and snapshot --- workflows/sra/tests/main.nf.test.snap | 2 +- .../sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +- .../tests/sra_custom_ena_metadata_fields.nf.test.snap | 10 +++++----- .../sra/tests/sra_force_sratools_download.nf.test | 2 +- .../sra/tests/sra_force_sratools_download.nf.test.snap | 6 +++--- .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 2 +- .../tests/sra_nf_core_pipeline_atacseq.nf.test.snap | 6 +++--- .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- .../sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 10 +++++----- .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- .../sra_nf_core_pipeline_taxprofiler.nf.test.snap | 10 +++++----- .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +- .../tests/sra_nf_core_pipeline_viralrecon.nf.test.snap | 6 +++--- workflows/sra/tests/sra_skip_fastq_download.nf.test | 2 +- .../sra/tests/sra_skip_fastq_download.nf.test.snap | 2 +- 15 files changed, 33 insertions(+), 33 deletions(-) diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 1692d4cd..b8dc88ca 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -1348,6 +1348,6 @@ ] } ], - "timestamp": "2023-09-11T18:23:09.598326" + "timestamp": "2023-09-11T18:56:05.693225" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 4dc9ba8b..45280ab0 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -16,7 +16,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "rnaseq" ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" sample_mapping_fields = "run_accession,library_layout" diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index c2782552..a2537a95 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -272,14 +272,14 @@ ] ], "1": [ - "samplesheet.csv:md5,7bca96e409bd9eb6790e0d6737af686c" + "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562" ], "2": [ "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" @@ -557,17 +557,17 @@ "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f" ], "samplesheet": [ - "samplesheet.csv:md5,7bca96e409bd9eb6790e0d6737af686c" + "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" ] } ], - "timestamp": "2023-09-11T16:47:26.813819" + "timestamp": "2023-09-11T18:48:18.757655" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 2b1b5953..76ce7cd3 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -16,7 +16,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" force_sratools_download = true } } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 2c779c84..4e1b8aaf 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -662,7 +662,7 @@ ] ], "1": [ - "samplesheet.csv:md5,9d4b95a31702af34a6f57d963137340d" + "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" ], "2": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" @@ -1336,7 +1336,7 @@ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "samplesheet": [ - "samplesheet.csv:md5,9d4b95a31702af34a6f57d963137340d" + "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" ], "versions": [ "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", @@ -1346,6 +1346,6 @@ ] } ], - "timestamp": "2023-09-11T17:03:59.154427" + "timestamp": "2023-09-11T19:02:05.556134" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 3d946fea..0ce0c230 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -16,7 +16,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "atacseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 069e3390..f6528e52 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -662,7 +662,7 @@ ] ], "1": [ - "samplesheet.csv:md5,252449b9f66687af076bb5a9dfea4551" + "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c" ], "2": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" @@ -1337,7 +1337,7 @@ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "samplesheet": [ - "samplesheet.csv:md5,252449b9f66687af076bb5a9dfea4551" + "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c" ], "versions": [ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", @@ -1348,6 +1348,6 @@ ] } ], - "timestamp": "2023-09-11T16:36:17.537997" + "timestamp": "2023-09-11T18:37:54.607231" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index f51aa4ca..67c0fbe4 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -16,7 +16,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "rnaseq" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 4c2abc45..124877ae 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -662,14 +662,14 @@ ] ], "1": [ - "samplesheet.csv:md5,f0b7e9436c6feb1a31c49c2c8ab761a2" + "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80" ], "2": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" @@ -1337,17 +1337,17 @@ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "samplesheet": [ - "samplesheet.csv:md5,f0b7e9436c6feb1a31c49c2c8ab761a2" + "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" ] } ], - "timestamp": "2023-09-11T16:53:44.32524" + "timestamp": "2023-09-11T18:51:38.198125" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 97cd4a44..e00793cd 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -16,7 +16,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "taxprofiler" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index a94fc295..b63ad4b7 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -662,14 +662,14 @@ ] ], "1": [ - "samplesheet.csv:md5,484efbb550b50f5ac63e4864282edea7" + "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c" ], "2": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" @@ -1337,17 +1337,17 @@ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "samplesheet": [ - "samplesheet.csv:md5,484efbb550b50f5ac63e4864282edea7" + "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" ] } ], - "timestamp": "2023-09-11T16:42:06.867767" + "timestamp": "2023-09-11T18:44:02.293186" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 434fac63..045e0363 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -16,7 +16,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" nf_core_pipeline = "viralrecon" } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 8b6be6a1..1387f422 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -662,7 +662,7 @@ ] ], "1": [ - "samplesheet.csv:md5,3e32e2cfa3c8b23c9cd32d91b885c0de" + "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" ], "2": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" @@ -1337,7 +1337,7 @@ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" ], "samplesheet": [ - "samplesheet.csv:md5,3e32e2cfa3c8b23c9cd32d91b885c0de" + "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" ], "versions": [ "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", @@ -1348,6 +1348,6 @@ ] } ], - "timestamp": "2023-09-11T16:33:01.320808" + "timestamp": "2023-09-11T18:34:25.049818" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index dbe40144..67abee3b 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -16,7 +16,7 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" + outdir = "results" skip_fastq_download = true } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index 921bed59..3b04b917 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -32,6 +32,6 @@ ] } ], - "timestamp": "2023-09-11T16:58:42.10055" + "timestamp": "2023-09-11T18:56:34.175665" } } \ No newline at end of file From 410321c8f88e2d28abd328e5d098d4780b76276d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 12:51:28 +0200 Subject: [PATCH 048/175] implement changes in GHA CI --- .github/workflows/ci.yml | 46 ++++++++++++++++++++++------------------ 1 file changed, 25 insertions(+), 21 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5c5df959..4fe23a91 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,18 +1,17 @@ # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors name: nf-core CI +# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: - push: - branches: - - dev - - refactor pull_request: + release: + types: [published] + merge_group: + types: + - checks_requested branches: - - dev - master + - dev - refactor - release: - types: - - "published" env: NXF_ANSI_LOG: false @@ -23,6 +22,19 @@ concurrency: cancel-in-progress: true jobs: + changes: + name: Check for changes + runs-on: ubuntu-latest + outputs: + # Expose matched filters as job 'tags' output variable + tags: ${{ steps.filter.outputs.changes }} + steps: + - uses: actions/checkout@v3 + - uses: dorny/paths-filter@v2 + id: filter + with: + filters: "tests/config/tags.yml" + define_nxf_versions: name: Choose nextflow versions to test against depending on target branch runs-on: ubuntu-latest @@ -38,23 +50,15 @@ jobs: fi test: - name: Run pipeline with test data - needs: define_nxf_versions + name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} + needs: [changes, define_nxf_versions] + if: needs.changes.outputs.tags != '[]' runs-on: ubuntu-latest strategy: fail-fast: false matrix: NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} - test_tags: - - "modules_local" - - "sra_default_parameters" - - "sra_custom_ena_metadata_fields" - - "sra_force_sratools_download" - - "sra_nf_core_pipeline_atacseq" - - "sra_nf_core_pipeline_rnaseq" - - "sra_nf_core_pipeline_taxprofiler" - - "sra_nf_core_pipeline_viralrecon" - - "sra_skip_fastq_download" + tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] profile: - "docker" @@ -74,7 +78,7 @@ jobs: - name: Run nf-test run: | - nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml + nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml - name: Output log on failure if: failure() From 57d6921e74bbfca14d021964bcd03723e42ad33c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 14:45:11 +0200 Subject: [PATCH 049/175] add tags --- .github/tags.yml | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 .github/tags.yml diff --git a/.github/tags.yml b/.github/tags.yml new file mode 100644 index 00000000..8fe923f5 --- /dev/null +++ b/.github/tags.yml @@ -0,0 +1,40 @@ +# local modules + +multiqc_mappings_config: + - modules/local/multiqc_mappings_config/* +sra_fastq_ftp: + - modules/local/sra_fastq_ftp/* +sra_ids_to_runinfo: + - modules/local/sra_ids_to_runinfo/* +sra_merge_samplesheet: + - modules/local/sra_merge_samplesheet/* +sra_runinfo_to_ftp: + - modules/local/sra_runinfo_to_ftp/* +sra_to_samplesheet: + - modules/local/sra_to_samplesheet/* + +# workflow: sra +sra_custom_ena_metadata_fields: + - conf/modules/sra.config + - workflows/sra/main.nf +sra_default_parameters: + - conf/modules/sra.config + - workflows/sra/main.nf +sra_force_sratools_download: + - conf/modules/sra.config + - workflows/sra/main.nf +sra_nf_core_pipeline_atacseq: + - conf/modules/sra.config + - workflows/sra/main.nf +sra_nf_core_pipeline_rnaseq: + - conf/modules/sra.config + - workflows/sra/main.nf +sra_nf_core_pipeline_taxprofiler: + - conf/modules/sra.config + - workflows/sra/main.nf +sra_nf_core_pipeline_viralrecon: + - conf/modules/sra.config + - workflows/sra/main.nf +sra_skip_fastq_download: + - conf/modules/sra.config + - workflows/sra/main.nf From e9d38bb614c8d93d2a8c542ff3d1ec53e3aed38d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 14:45:19 +0200 Subject: [PATCH 050/175] fix path to tags --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4fe23a91..7b7070e7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,7 +33,7 @@ jobs: - uses: dorny/paths-filter@v2 id: filter with: - filters: "tests/config/tags.yml" + filters: ".github/tags.yml" define_nxf_versions: name: Choose nextflow versions to test against depending on target branch From 54f954ca4371ea42f3e5cc0610cd747eb111bf3b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 15:16:10 +0200 Subject: [PATCH 051/175] rename files --- .../sra/tests/{main.nf.test => sra_default_parameters.nf.test} | 0 .../{main.nf.test.snap => sra_default_parameters.nf.test.snap} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename workflows/sra/tests/{main.nf.test => sra_default_parameters.nf.test} (100%) rename workflows/sra/tests/{main.nf.test.snap => sra_default_parameters.nf.test.snap} (100%) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/sra_default_parameters.nf.test similarity index 100% rename from workflows/sra/tests/main.nf.test rename to workflows/sra/tests/sra_default_parameters.nf.test diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap similarity index 100% rename from workflows/sra/tests/main.nf.test.snap rename to workflows/sra/tests/sra_default_parameters.nf.test.snap From 82510e8b9297fb1106cf86c4e191cfedbd6c4101 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 15:16:19 +0200 Subject: [PATCH 052/175] add tests to tags --- .github/tags.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/tags.yml b/.github/tags.yml index 8fe923f5..68607d79 100644 --- a/.github/tags.yml +++ b/.github/tags.yml @@ -1,5 +1,4 @@ # local modules - multiqc_mappings_config: - modules/local/multiqc_mappings_config/* sra_fastq_ftp: @@ -16,25 +15,33 @@ sra_to_samplesheet: # workflow: sra sra_custom_ena_metadata_fields: - conf/modules/sra.config + - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test - workflows/sra/main.nf sra_default_parameters: - conf/modules/sra.config + - workflows/sra/tests/sra_default_parameters.nf.test - workflows/sra/main.nf sra_force_sratools_download: - conf/modules/sra.config + - workflows/sra/tests/sra_force_sratools_download.nf.test - workflows/sra/main.nf sra_nf_core_pipeline_atacseq: - conf/modules/sra.config + - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test - workflows/sra/main.nf sra_nf_core_pipeline_rnaseq: - conf/modules/sra.config + - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test - workflows/sra/main.nf sra_nf_core_pipeline_taxprofiler: - conf/modules/sra.config + - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test - workflows/sra/main.nf sra_nf_core_pipeline_viralrecon: - conf/modules/sra.config + - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test - workflows/sra/main.nf sra_skip_fastq_download: - conf/modules/sra.config + - workflows/sra/tests/sra_skip_fastq_download.nf.test - workflows/sra/main.nf From c707eef5871a8a82bdfc1b6f3f918ced7b0b252f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 15:24:45 +0200 Subject: [PATCH 053/175] alphabetical order --- .github/tags.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/tags.yml b/.github/tags.yml index 68607d79..aa7b69c9 100644 --- a/.github/tags.yml +++ b/.github/tags.yml @@ -15,33 +15,33 @@ sra_to_samplesheet: # workflow: sra sra_custom_ena_metadata_fields: - conf/modules/sra.config - - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test - workflows/sra/main.nf + - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test sra_default_parameters: - conf/modules/sra.config - - workflows/sra/tests/sra_default_parameters.nf.test - workflows/sra/main.nf + - workflows/sra/tests/sra_default_parameters.nf.test sra_force_sratools_download: - conf/modules/sra.config - - workflows/sra/tests/sra_force_sratools_download.nf.test - workflows/sra/main.nf + - workflows/sra/tests/sra_force_sratools_download.nf.test sra_nf_core_pipeline_atacseq: - conf/modules/sra.config - - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test - workflows/sra/main.nf + - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test sra_nf_core_pipeline_rnaseq: - conf/modules/sra.config - - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test - workflows/sra/main.nf + - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test sra_nf_core_pipeline_taxprofiler: - conf/modules/sra.config - - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test - workflows/sra/main.nf + - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test sra_nf_core_pipeline_viralrecon: - conf/modules/sra.config - - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test - workflows/sra/main.nf + - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test sra_skip_fastq_download: - conf/modules/sra.config - - workflows/sra/tests/sra_skip_fastq_download.nf.test - workflows/sra/main.nf + - workflows/sra/tests/sra_skip_fastq_download.nf.test From b5d80fb8ad782d6366fa77cc41bde11000f257c4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 12 Sep 2023 15:33:28 +0200 Subject: [PATCH 054/175] add modules to changes --- .github/tags.yml | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/.github/tags.yml b/.github/tags.yml index aa7b69c9..ed5c9dcc 100644 --- a/.github/tags.yml +++ b/.github/tags.yml @@ -15,33 +15,73 @@ sra_to_samplesheet: # workflow: sra sra_custom_ena_metadata_fields: - conf/modules/sra.config + - modules/local/sra_ids_to_runinfo/main.nf + - modules/local/sra_runinfo_to_ftp/main.nf + - modules/local/sra_fastq_ftp/main.nf + - modules/local/sra_to_samplesheet/main.nf + - modules/local/sra_merge_samplesheet/main.nf - workflows/sra/main.nf - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test sra_default_parameters: - conf/modules/sra.config + - modules/local/sra_ids_to_runinfo/main.nf + - modules/local/sra_runinfo_to_ftp/main.nf + - modules/local/sra_fastq_ftp/main.nf + - modules/local/sra_to_samplesheet/main.nf + - modules/local/sra_merge_samplesheet/main.nf - workflows/sra/main.nf - workflows/sra/tests/sra_default_parameters.nf.test sra_force_sratools_download: - conf/modules/sra.config + - modules/local/sra_ids_to_runinfo/main.nf + - modules/local/sra_runinfo_to_ftp/main.nf + - modules/local/sra_fastq_ftp/main.nf + - modules/local/sra_to_samplesheet/main.nf + - modules/local/sra_merge_samplesheet/main.nf - workflows/sra/main.nf - workflows/sra/tests/sra_force_sratools_download.nf.test sra_nf_core_pipeline_atacseq: - conf/modules/sra.config + - modules/local/sra_ids_to_runinfo/main.nf + - modules/local/sra_runinfo_to_ftp/main.nf + - modules/local/sra_fastq_ftp/main.nf + - modules/local/sra_to_samplesheet/main.nf + - modules/local/sra_merge_samplesheet/main.nf - workflows/sra/main.nf - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test sra_nf_core_pipeline_rnaseq: - conf/modules/sra.config + - modules/local/sra_ids_to_runinfo/main.nf + - modules/local/sra_runinfo_to_ftp/main.nf + - modules/local/sra_fastq_ftp/main.nf + - modules/local/sra_to_samplesheet/main.nf + - modules/local/sra_merge_samplesheet/main.nf - workflows/sra/main.nf - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test sra_nf_core_pipeline_taxprofiler: - conf/modules/sra.config + - modules/local/sra_ids_to_runinfo/main.nf + - modules/local/sra_runinfo_to_ftp/main.nf + - modules/local/sra_fastq_ftp/main.nf + - modules/local/sra_to_samplesheet/main.nf + - modules/local/sra_merge_samplesheet/main.nf - workflows/sra/main.nf - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test sra_nf_core_pipeline_viralrecon: - conf/modules/sra.config + - modules/local/sra_ids_to_runinfo/main.nf + - modules/local/sra_runinfo_to_ftp/main.nf + - modules/local/sra_fastq_ftp/main.nf + - modules/local/sra_to_samplesheet/main.nf + - modules/local/sra_merge_samplesheet/main.nf - workflows/sra/main.nf - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test sra_skip_fastq_download: - conf/modules/sra.config + - modules/local/sra_ids_to_runinfo/main.nf + - modules/local/sra_runinfo_to_ftp/main.nf + - modules/local/sra_fastq_ftp/main.nf + - modules/local/sra_to_samplesheet/main.nf + - modules/local/sra_merge_samplesheet/main.nf - workflows/sra/main.nf - workflows/sra/tests/sra_skip_fastq_download.nf.test From 9c6bf658cfeba3b1780615faa794f77d85c44000 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 14:57:33 +0100 Subject: [PATCH 055/175] Remove public_aws_ecr profile --- .github/workflows/cloud_tests_full.yml | 2 +- .github/workflows/cloud_tests_small.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml index e25a97aa..d0ed0552 100644 --- a/.github/workflows/cloud_tests_full.yml +++ b/.github/workflows/cloud_tests_full.yml @@ -27,7 +27,7 @@ jobs: compute_env: ${{ secrets.TOWER_CE_AWS_CPU }} workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}" run_name: "aws_fetchngs_full" - profiles: test_full,public_aws_ecr + profiles: test_full parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml index e7636fdc..12b8daab 100644 --- a/.github/workflows/cloud_tests_small.yml +++ b/.github/workflows/cloud_tests_small.yml @@ -25,7 +25,7 @@ jobs: compute_env: ${{ secrets.TOWER_CE_AWS_CPU }} workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}" run_name: "aws_fetchngs_small" - profiles: test,public_aws_ecr + profiles: test parameters: | { "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}" From 2c7c13f08909ea069bb0dbb86ed78874f40f38a5 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 15:02:36 +0100 Subject: [PATCH 056/175] Replace large config file with individual configs per module --- conf/modules/sra.config | 88 ------------------- .../multiqc_mappings_config/nextflow.config | 9 ++ modules/local/sra_fastq_ftp/nextflow.config | 17 ++++ .../local/sra_ids_to_runinfo/nextflow.config | 8 ++ .../sra_merge_samplesheet/nextflow.config | 9 ++ .../local/sra_runinfo_to_ftp/nextflow.config | 9 ++ .../local/sra_to_samplesheet/nextflow.config | 8 ++ .../sratools/fasterqdump/nextflow.config | 10 +++ .../nf-core/sratools/prefetch/nextflow.config | 8 ++ nextflow.config | 2 +- workflows/sra/nextflow.config | 7 ++ workflows/synapse/nextflow.config | 0 12 files changed, 86 insertions(+), 89 deletions(-) delete mode 100644 conf/modules/sra.config create mode 100644 modules/local/multiqc_mappings_config/nextflow.config create mode 100644 modules/local/sra_fastq_ftp/nextflow.config create mode 100644 modules/local/sra_ids_to_runinfo/nextflow.config create mode 100644 modules/local/sra_merge_samplesheet/nextflow.config create mode 100644 modules/local/sra_runinfo_to_ftp/nextflow.config create mode 100644 modules/local/sra_to_samplesheet/nextflow.config create mode 100644 modules/nf-core/sratools/fasterqdump/nextflow.config create mode 100644 modules/nf-core/sratools/prefetch/nextflow.config create mode 100644 workflows/sra/nextflow.config create mode 100644 workflows/synapse/nextflow.config diff --git a/conf/modules/sra.config b/conf/modules/sra.config deleted file mode 100644 index 15802b41..00000000 --- a/conf/modules/sra.config +++ /dev/null @@ -1,88 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. ----------------------------------------------------------------------------------------- -*/ - -// -// Process options for the SRA workflow -// -process { - - withName: SRA_IDS_TO_RUNINFO { - publishDir = [ - path: { "${params.outdir}/metadata" }, - enabled: false - ] - } - - withName: SRA_RUNINFO_TO_FTP { - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SRA_FASTQ_FTP { - ext.args = '--retry 5 --continue-at - --max-time 1200' - publishDir = [ - [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ], - [ - path: { "${params.outdir}/fastq/md5" }, - mode: params.publish_dir_mode, - pattern: "*.md5" - ] - ] - } - - withName: SRATOOLS_PREFETCH { - publishDir = [ - path: { "${params.outdir}/sra" }, - enabled: false - ] - } - - withName: SRATOOLS_FASTERQDUMP { - ext.args = '--split-files --include-technical' - publishDir = [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ] - } - - withName: SRA_TO_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - enabled: false - ] - } - - withName: SRA_MERGE_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: MULTIQC_MAPPINGS_CONFIG { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - -} diff --git a/modules/local/multiqc_mappings_config/nextflow.config b/modules/local/multiqc_mappings_config/nextflow.config new file mode 100644 index 00000000..e2382930 --- /dev/null +++ b/modules/local/multiqc_mappings_config/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'MULTIQC_MAPPINGS_CONFIG' { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/nextflow.config b/modules/local/sra_fastq_ftp/nextflow.config new file mode 100644 index 00000000..7b5ebf70 --- /dev/null +++ b/modules/local/sra_fastq_ftp/nextflow.config @@ -0,0 +1,17 @@ +process { + withName: 'SRA_FASTQ_FTP' { + ext.args = '--retry 5 --continue-at - --max-time 1200' + publishDir = [ + [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ], + [ + path: { "${params.outdir}/fastq/md5" }, + mode: params.publish_dir_mode, + pattern: "*.md5" + ] + ] + } +} diff --git a/modules/local/sra_ids_to_runinfo/nextflow.config b/modules/local/sra_ids_to_runinfo/nextflow.config new file mode 100644 index 00000000..73da969a --- /dev/null +++ b/modules/local/sra_ids_to_runinfo/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: 'SRA_IDS_TO_RUNINFO' { + publishDir = [ + path: { "${params.outdir}/metadata" }, + enabled: false + ] + } +} \ No newline at end of file diff --git a/modules/local/sra_merge_samplesheet/nextflow.config b/modules/local/sra_merge_samplesheet/nextflow.config new file mode 100644 index 00000000..f2926529 --- /dev/null +++ b/modules/local/sra_merge_samplesheet/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'SRA_MERGE_SAMPLESHEET' { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/nextflow.config b/modules/local/sra_runinfo_to_ftp/nextflow.config new file mode 100644 index 00000000..aee1848c --- /dev/null +++ b/modules/local/sra_runinfo_to_ftp/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'SRA_RUNINFO_TO_FTP' { + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/nextflow.config b/modules/local/sra_to_samplesheet/nextflow.config new file mode 100644 index 00000000..da241c1a --- /dev/null +++ b/modules/local/sra_to_samplesheet/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: SRA_TO_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + enabled: false + ] + } +} diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config new file mode 100644 index 00000000..f98b140d --- /dev/null +++ b/modules/nf-core/sratools/fasterqdump/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: SRATOOLS_FASTERQDUMP { + ext.args = '--split-files --include-technical' + publishDir = [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config new file mode 100644 index 00000000..a2ca8848 --- /dev/null +++ b/modules/nf-core/sratools/prefetch/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: SRATOOLS_PREFETCH { + publishDir = [ + path: { "${params.outdir}/sra" }, + enabled: false + ] + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index e2584ce6..40149dba 100644 --- a/nextflow.config +++ b/nextflow.config @@ -219,7 +219,7 @@ manifest { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules/base.config' if ( params.input_type == 'sra' ) { - includeConfig 'conf/modules/sra.config' + includeConfig 'workflows/sra/nextflow.config' } if ( params.input_type == 'synapse' ) { includeConfig 'conf/modules/synapse.config' diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config new file mode 100644 index 00000000..d4dd6f30 --- /dev/null +++ b/workflows/sra/nextflow.config @@ -0,0 +1,7 @@ +includeConfig "../../modules/local/multiqc_mappings_config/nextflow.config" +includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config" +includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config" +includeConfig "../../modules/local/sra_merge_samplesheet/nextflow.config" +includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config" +includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config" +includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config" diff --git a/workflows/synapse/nextflow.config b/workflows/synapse/nextflow.config new file mode 100644 index 00000000..e69de29b From 64aca64197641d7f36df4b3be2ce25c200a42293 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:17:33 +0100 Subject: [PATCH 057/175] Inherit Synapse related configuration via separate files --- conf/modules/synapse.config | 66 ------------------- modules/local/synapse_get/nextflow.config | 16 +++++ modules/local/synapse_list/nextflow.config | 10 +++ .../synapse_merge_samplesheet/nextflow.config | 9 +++ modules/local/synapse_show/nextflow.config | 9 +++ .../synapse_to_samplesheet/nextflow.config | 8 +++ nextflow.config | 11 ++-- workflows/synapse/nextflow.config | 5 ++ 8 files changed, 63 insertions(+), 71 deletions(-) delete mode 100644 conf/modules/synapse.config create mode 100644 modules/local/synapse_get/nextflow.config create mode 100644 modules/local/synapse_list/nextflow.config create mode 100644 modules/local/synapse_merge_samplesheet/nextflow.config create mode 100644 modules/local/synapse_show/nextflow.config create mode 100644 modules/local/synapse_to_samplesheet/nextflow.config diff --git a/conf/modules/synapse.config b/conf/modules/synapse.config deleted file mode 100644 index 2f52aa6f..00000000 --- a/conf/modules/synapse.config +++ /dev/null @@ -1,66 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. ----------------------------------------------------------------------------------------- -*/ - -// -// Process options for the Synapse workflow -// - -process { - - withName: SYNAPSE_LIST { - ext.args = '--long' - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SYNAPSE_GET { - publishDir = [ - [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ], - [ - path: { "${params.outdir}/fastq/md5" }, - mode: params.publish_dir_mode, - pattern: "*.md5" - ] - ] - } - - withName: SYNAPSE_SHOW { - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SYNAPSE_TO_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - enabled: false - ] - } - - withName: SYNAPSE_MERGE_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - -} diff --git a/modules/local/synapse_get/nextflow.config b/modules/local/synapse_get/nextflow.config new file mode 100644 index 00000000..869f80aa --- /dev/null +++ b/modules/local/synapse_get/nextflow.config @@ -0,0 +1,16 @@ +process { + withName: 'SYNAPSE_GET' { + publishDir = [ + [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ], + [ + path: { "${params.outdir}/fastq/md5" }, + mode: params.publish_dir_mode, + pattern: "*.md5" + ] + ] + } +} \ No newline at end of file diff --git a/modules/local/synapse_list/nextflow.config b/modules/local/synapse_list/nextflow.config new file mode 100644 index 00000000..15124234 --- /dev/null +++ b/modules/local/synapse_list/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: SYNAPSE_LIST { + ext.args = '--long' + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} diff --git a/modules/local/synapse_merge_samplesheet/nextflow.config b/modules/local/synapse_merge_samplesheet/nextflow.config new file mode 100644 index 00000000..9befef9c --- /dev/null +++ b/modules/local/synapse_merge_samplesheet/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: SYNAPSE_MERGE_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/synapse_show/nextflow.config b/modules/local/synapse_show/nextflow.config new file mode 100644 index 00000000..a1864dfe --- /dev/null +++ b/modules/local/synapse_show/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'SYNAPSE_SHOW' { + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/synapse_to_samplesheet/nextflow.config b/modules/local/synapse_to_samplesheet/nextflow.config new file mode 100644 index 00000000..b286c12c --- /dev/null +++ b/modules/local/synapse_to_samplesheet/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: SYNAPSE_TO_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + enabled: false + ] + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 40149dba..4ee1bb88 100644 --- a/nextflow.config +++ b/nextflow.config @@ -218,11 +218,12 @@ manifest { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules/base.config' -if ( params.input_type == 'sra' ) { - includeConfig 'workflows/sra/nextflow.config' -} -if ( params.input_type == 'synapse' ) { - includeConfig 'conf/modules/synapse.config' + +switch ( params.input_type ) { + case "sra": + includeConfig './workflows/sra/nextflow.config' + case "synapse": + includeConfig './workflows/synapse/nextflow.config' } // Function to ensure that resource requirements don't go beyond diff --git a/workflows/synapse/nextflow.config b/workflows/synapse/nextflow.config index e69de29b..01b71558 100644 --- a/workflows/synapse/nextflow.config +++ b/workflows/synapse/nextflow.config @@ -0,0 +1,5 @@ +includeConfig "../../modules/local/synapse_get/nextflow.config" +includeConfig "../../modules/local/synapse_to_samplesheet/nextflow.config" +includeConfig "../../modules/local/synapse_list/nextflow.config" +includeConfig "../../modules/local/synapse_merge_samplesheet/nextflow.config" +includeConfig "../../modules/local/synapse_show/nextflow.config" \ No newline at end of file From 63caf19616aacac49992ac058bff13b9fa60bb3e Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:23:54 +0100 Subject: [PATCH 058/175] Revert switch for inheritance of correct config --- nextflow.config | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/nextflow.config b/nextflow.config index 4ee1bb88..84d8b42e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -219,11 +219,10 @@ manifest { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules/base.config' -switch ( params.input_type ) { - case "sra": - includeConfig './workflows/sra/nextflow.config' - case "synapse": - includeConfig './workflows/synapse/nextflow.config' +if ( params.input_type == "sra" ) { + includeConfig './workflows/sra/nextflow.config' +} else if ( params.input_type == "synapse" ) { + includeConfig './workflows/synapse/nextflow.config' } // Function to ensure that resource requirements don't go beyond From 1dba48c4a0d95bac089557a552ac5d17fcb08393 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:36:14 +0100 Subject: [PATCH 059/175] Handle custom/dumpsoftwareversions via config --- conf/base.config | 9 ++++++--- conf/modules/base.config | 1 + modules/nf-core/custom/nextflow.config | 10 ++++++++++ nextflow.config | 4 ++-- workflows/nextflow.config | 15 +++++++++++++++ 5 files changed, 34 insertions(+), 5 deletions(-) create mode 100644 modules/nf-core/custom/nextflow.config create mode 100644 workflows/nextflow.config diff --git a/conf/base.config b/conf/base.config index 4767e522..6af79a7b 100644 --- a/conf/base.config +++ b/conf/base.config @@ -14,6 +14,12 @@ process { memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } + publishDir = [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' @@ -57,7 +63,4 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - } } diff --git a/conf/modules/base.config b/conf/modules/base.config index d7eb6c86..035487c5 100644 --- a/conf/modules/base.config +++ b/conf/modules/base.config @@ -22,6 +22,7 @@ process { ] withName: CUSTOM_DUMPSOFTWAREVERSIONS { + cache = false publishDir = [ path: { "${params.outdir}/pipeline_info" }, mode: params.publish_dir_mode, diff --git a/modules/nf-core/custom/nextflow.config b/modules/nf-core/custom/nextflow.config new file mode 100644 index 00000000..241654e7 --- /dev/null +++ b/modules/nf-core/custom/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: CUSTOM_DUMPSOFTWAREVERSIONS { + cache = false + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: params.publish_dir_mode, + pattern: '*_versions.yml' + ] + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 84d8b42e..a11a769d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -216,8 +216,8 @@ manifest { doi = 'https://doi.org/10.5281/zenodo.5070524' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules/base.config' +// Module specific configs +includeConfig 'modules/nf-core/custom/nextflow.config' if ( params.input_type == "sra" ) { includeConfig './workflows/sra/nextflow.config' diff --git a/workflows/nextflow.config b/workflows/nextflow.config new file mode 100644 index 00000000..db80204c --- /dev/null +++ b/workflows/nextflow.config @@ -0,0 +1,15 @@ +process { + publishDir = [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + + withName: CUSTOM_DUMPSOFTWAREVERSIONS { + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: params.publish_dir_mode, + pattern: '*_versions.yml' + ] + } +} From f86a80ba422bf993783988ecf46c1485ea262e1f Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:37:18 +0100 Subject: [PATCH 060/175] Update multiqc to v1.15 --- modules.json | 2 +- modules/nf-core/custom/dumpsoftwareversions/main.nf | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules.json b/modules.json index 3137b88b..ab610dfb 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions From 31e10bb27f66dd6fe6ec8bd8d92935b31434df3b Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:39:20 +0100 Subject: [PATCH 061/175] Use switch statement to avoid nested if-else --- nextflow.config | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/nextflow.config b/nextflow.config index a11a769d..dc2a5d2b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -219,11 +219,24 @@ manifest { // Module specific configs includeConfig 'modules/nf-core/custom/nextflow.config' +/* if ( params.input_type == "sra" ) { includeConfig './workflows/sra/nextflow.config' } else if ( params.input_type == "synapse" ) { includeConfig './workflows/synapse/nextflow.config' } +*/ + +switch ( params.input_type ) { + case "sra": + includeConfig './workflows/sra/nextflow.config' + break + case "synapse": + includeConfig './workflows/synapse/nextflow.config' + break + default: + break +} // Function to ensure that resource requirements don't go beyond // a maximum limit From 105a65f8597b18b4397e6e075153090f9244d604 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:44:42 +0100 Subject: [PATCH 062/175] Moved workflows configuration to workflows/nextflow.config --- .../nextflow.config | 0 nextflow.config | 23 +++-------------- workflows/nextflow.config | 25 ++++++++----------- 3 files changed, 15 insertions(+), 33 deletions(-) rename modules/nf-core/custom/{ => dumpsoftwareversions}/nextflow.config (100%) diff --git a/modules/nf-core/custom/nextflow.config b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config similarity index 100% rename from modules/nf-core/custom/nextflow.config rename to modules/nf-core/custom/dumpsoftwareversions/nextflow.config diff --git a/nextflow.config b/nextflow.config index dc2a5d2b..4fad92ca 100644 --- a/nextflow.config +++ b/nextflow.config @@ -217,26 +217,11 @@ manifest { } // Module specific configs -includeConfig 'modules/nf-core/custom/nextflow.config' +// Currently just dumpsoftwareversions +includeConfig 'modules/nf-core/custom/dumpsoftwareversions/nextflow.config' -/* -if ( params.input_type == "sra" ) { - includeConfig './workflows/sra/nextflow.config' -} else if ( params.input_type == "synapse" ) { - includeConfig './workflows/synapse/nextflow.config' -} -*/ - -switch ( params.input_type ) { - case "sra": - includeConfig './workflows/sra/nextflow.config' - break - case "synapse": - includeConfig './workflows/synapse/nextflow.config' - break - default: - break -} +// Workflow specific configs +includeConfig 'workflows/nextflow.config' // Function to ensure that resource requirements don't go beyond // a maximum limit diff --git a/workflows/nextflow.config b/workflows/nextflow.config index db80204c..d27deb3a 100644 --- a/workflows/nextflow.config +++ b/workflows/nextflow.config @@ -1,15 +1,12 @@ -process { - publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] +// Read in specific config relating to workflow. - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } -} +switch ( params.input_type ) { + case "sra": + includeConfig './sra/nextflow.config' + break + case "synapse": + includeConfig './synapse/nextflow.config' + break + default: + break +} \ No newline at end of file From 8b256afb6466d3834488adf9b8e58cf334bff6b7 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:55:39 +0100 Subject: [PATCH 063/175] Addition of subworkflow specific configuration file --- .../nextflow.config | 2 ++ workflows/sra/nextflow.config | 1 + 2 files changed, 3 insertions(+) create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config new file mode 100644 index 00000000..b11c499f --- /dev/null +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config @@ -0,0 +1,2 @@ +includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config' +includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config' \ No newline at end of file diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config index d4dd6f30..6b66fcd5 100644 --- a/workflows/sra/nextflow.config +++ b/workflows/sra/nextflow.config @@ -5,3 +5,4 @@ includeConfig "../../modules/local/sra_merge_samplesheet/nextflow.config" includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config" includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config" includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config" +includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config" From 57b46e4d93b7d463f1d6079c8d88f73611690314 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:57:25 +0100 Subject: [PATCH 064/175] Add empty config for sratoolsncbisettings to make it consistent --- modules/nf-core/custom/sratoolsncbisettings/nextflow.config | 0 .../nextflow.config | 3 ++- 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/custom/sratoolsncbisettings/nextflow.config diff --git a/modules/nf-core/custom/sratoolsncbisettings/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/nextflow.config new file mode 100644 index 00000000..e69de29b diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config index b11c499f..996c1888 100644 --- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config @@ -1,2 +1,3 @@ includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config' -includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config' \ No newline at end of file +includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config' +includeConfig '../../../modules/nf-core/custom/sratoolsncbisettings/nextflow.config' \ No newline at end of file From 32561205d47040660d539cdd9a37a1bc4d50a3b5 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 17:07:55 +0100 Subject: [PATCH 065/175] CHANGELOG --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 20dd21f8..92e31da4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Enhancements & fixes - [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests -- [#184](https://github.com/nf-core/fetchngs/pull/184/files) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow) +- [#184](https://github.com/nf-core/fetchngs/pull/184) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow) +- [#195](https://github.com/nf-core/fetchngs/pull/195) Separate configuration files for all modules ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16 From 8284cc4003a71307d7e5eacf4e028eb72c23da7b Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 18 Sep 2023 17:09:51 +0100 Subject: [PATCH 066/175] Update change tags --- .github/tags.yml | 104 ++++++++++++++++++++++------------------------- 1 file changed, 48 insertions(+), 56 deletions(-) diff --git a/.github/tags.yml b/.github/tags.yml index ed5c9dcc..9fc74a2c 100644 --- a/.github/tags.yml +++ b/.github/tags.yml @@ -14,74 +14,66 @@ sra_to_samplesheet: # workflow: sra sra_custom_ena_metadata_fields: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test sra_default_parameters: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_default_parameters.nf.test sra_force_sratools_download: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_force_sratools_download.nf.test sra_nf_core_pipeline_atacseq: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test sra_nf_core_pipeline_rnaseq: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test sra_nf_core_pipeline_taxprofiler: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test sra_nf_core_pipeline_viralrecon: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test sra_skip_fastq_download: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_skip_fastq_download.nf.test From 131788e37a7519a7fc35efa9b6fbd9d1ff919def Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 17:36:54 +0200 Subject: [PATCH 067/175] restore nf-test tests for sra workflow --- .../sra_custom_ena_metadata_fields.nf.test | 33 + ...ra_custom_ena_metadata_fields.nf.test.snap | 573 +++++++ .../sra/tests/sra_default_parameters.nf.test | 30 + .../tests/sra_default_parameters.nf.test.snap | 1353 +++++++++++++++++ .../tests/sra_force_sratools_download.nf.test | 31 + .../sra_force_sratools_download.nf.test.snap | 1351 ++++++++++++++++ .../sra_nf_core_pipeline_atacseq.nf.test | 31 + .../sra_nf_core_pipeline_atacseq.nf.test.snap | 1353 +++++++++++++++++ .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 31 + .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 1353 +++++++++++++++++ .../sra_nf_core_pipeline_taxprofiler.nf.test | 31 + ..._nf_core_pipeline_taxprofiler.nf.test.snap | 1353 +++++++++++++++++ .../sra_nf_core_pipeline_viralrecon.nf.test | 31 + ...a_nf_core_pipeline_viralrecon.nf.test.snap | 1353 +++++++++++++++++ .../sra/tests/sra_skip_fastq_download.nf.test | 31 + .../sra_skip_fastq_download.nf.test.snap | 37 + 16 files changed, 8975 insertions(+) create mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test create mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap create mode 100644 workflows/sra/tests/sra_default_parameters.nf.test create mode 100644 workflows/sra/tests/sra_default_parameters.nf.test.snap create mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test create mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test new file mode 100644 index 00000000..45280ab0 --- /dev/null +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -0,0 +1,33 @@ +nextflow_workflow { + + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" + tag "workflows" + tag "workflows_sra" + tag "sra_custom_ena_metadata_fields" + + test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { + + when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } + params { + outdir = "results" + nf_core_pipeline = "rnaseq" + ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" + sample_mapping_fields = "run_accession,library_layout" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap new file mode 100644 index 00000000..a2537a95 --- /dev/null +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -0,0 +1,573 @@ +{ + "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "library_layout": "SINGLE", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz", + "fastq_md5": 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assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap new file mode 100644 index 00000000..b8dc88ca --- /dev/null +++ b/workflows/sra/tests/sra_default_parameters.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: default": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": "GENOMIC", + "library_strategy": "OTHER", + 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assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap new file mode 100644 index 00000000..4e1b8aaf --- /dev/null +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -0,0 +1,1351 @@ +{ + "Parameters: --force_sratools_download": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": 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snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap new file mode 100644 index 00000000..f6528e52 --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: --nf_core_pipeline atacseq": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": "GENOMIC", + "library_strategy": "OTHER", + 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assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap new file mode 100644 index 00000000..124877ae --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: --nf_core_pipeline rnaseq": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": 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"taxprofiler" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap new file mode 100644 index 00000000..b63ad4b7 --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: --nf_core_pipeline taxprofiler": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + 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"read_count": "91", + "tax_id": "408170", + "scientific_name": "human gut metagenome", + "sample_title": "Metagenome or environmental sample from human gut metagenome", + "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", + "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", + "sample_description": "Metagenome or environmental sample from human gut metagenome", + "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98", + "fastq_bytes": "15420;16324", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz", + "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98", + "single_end": false + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "mappings": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "samplesheet": [ + "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + ], + "versions": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ] + } + ], + "timestamp": "2023-09-11T18:34:25.049818" + } +} \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test new file mode 100644 index 00000000..67abee3b --- /dev/null +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -0,0 +1,31 @@ +nextflow_workflow { + + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" + tag "workflows" + tag "workflows_sra" + tag "sra_skip_fastq_download" + + test("Parameters: --skip_fastq_download") { + + when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } + params { + outdir = "results" + skip_fastq_download = true + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap new file mode 100644 index 00000000..3b04b917 --- /dev/null +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -0,0 +1,37 @@ +{ + "Parameters: --skip_fastq_download": { + "content": [ + { + "0": [ + + ], + "1": [ + "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + ], + "2": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "3": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ], + "fastq": [ + + ], + "mappings": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "samplesheet": [ + "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + ], + "versions": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ] + } + ], + "timestamp": "2023-09-11T18:56:34.175665" + } +} \ No newline at end of file From 23b75bc70aa22c2d1dd66ce0d1ff3c0ed1a4ff6c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 19:21:10 +0200 Subject: [PATCH 068/175] restore module tests --- .../tests/main.nf.test | 31 ++++ .../tests/main.nf.test.snap | 52 +++++++ .../local/sra_fastq_ftp/tests/main.nf.test | 34 +++++ .../sra_fastq_ftp/tests/main.nf.test.snap | 140 ++++++++++++++++++ .../sra_ids_to_runinfo/tests/main.nf.test | 32 ++++ .../tests/main.nf.test.snap | 21 +++ .../sra_merge_samplesheet/tests/main.nf.test | 32 ++++ .../tests/main.nf.test.snap | 27 ++++ .../sra_runinfo_to_ftp/tests/main.nf.test | 31 ++++ .../tests/main.nf.test.snap | 21 +++ .../sra_to_samplesheet/tests/main.nf.test | 34 +++++ .../tests/main.nf.test.snap | 113 ++++++++++++++ 12 files changed, 568 insertions(+) create mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test create mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test.snap create mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test create mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test.snap create mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test create mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap create mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test create mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test.snap create mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test create mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap create mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test create mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test.snap diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test new file mode 100644 index 00000000..3bf79537 --- /dev/null +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -0,0 +1,31 @@ +nextflow_process { + + name "Test process: MULTIQC_MAPPINGS_CONFIG" + script "modules/local/multiqc_mappings_config/main.nf" + process "MULTIQC_MAPPINGS_CONFIG" + tag "modules" + tag "modules_local" + tag "multiqc_mappings_config" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap new file mode 100644 index 00000000..9cf7fb38 --- /dev/null +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -0,0 +1,52 @@ +{ + "SRX9626017_SRR13191702": { + "content": [ + { + "0": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ], + "1": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "versions": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "yml": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ] + } + ], + "timestamp": "2023-08-17T12:02:35+0000" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ], + "1": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "versions": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "yml": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ] + } + ], + "timestamp": "2023-08-17T12:02:35+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test new file mode 100644 index 00000000..7892d156 --- /dev/null +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test process: SRA_FASTQ_FTP" + script "modules/local/sra_fastq_ftp/main.nf" + process "SRA_FASTQ_FTP" + tag "modules" + tag "modules_local" + tag "sra_fastq_ftp" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = [ + [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map + params.test_data['modules_local']['sra_fastq_ftp'] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap new file mode 100644 index 00000000..c0d5ffdc --- /dev/null +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -0,0 +1,140 @@ +{ + "SRX9626017_SRR13191702": { + "content": [ + { + "0": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "1": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] + ], + "2": [ + "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" + ], + "fastq": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "md5": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] + ], + "versions": [ + "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" + ] + } + ], + "timestamp": "2023-08-06T23:31:57+0000" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "1": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] + ], + "2": [ + "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" + ], + "fastq": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "md5": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] + ], + "versions": [ + "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" + ] + } + ], + "timestamp": "2023-08-06T23:31:57+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test new file mode 100644 index 00000000..f8a44086 --- /dev/null +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test process: SRA_IDS_TO_RUNINFO" + script "modules/local/sra_ids_to_runinfo/main.nf" + process "SRA_IDS_TO_RUNINFO" + tag "modules" + tag "modules_local" + tag "sra_ids_to_runinfo" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = 'SRR13191702' + input[1] = '' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap new file mode 100644 index 00000000..dbca931f --- /dev/null +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" + ], + "1": [ + "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" + ], + "tsv": [ + "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" + ], + "versions": [ + "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" + ] + } + ], + "timestamp": "2023-08-06T23:30:51+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test new file mode 100644 index 00000000..e37039bd --- /dev/null +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test process: SRA_MERGE_SAMPLESHEET" + script "modules/local/sra_merge_samplesheet/main.nf" + process "SRA_MERGE_SAMPLESHEET" + tag "modules" + tag "modules_local" + tag "sra_merge_samplesheet" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) } + input[1] = params.test_data['modules_local']['sra_merge_samplesheet_mappings'].collect { file(it, checkIfExists: true) } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap new file mode 100644 index 00000000..c5f06aac --- /dev/null +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2" + ], + "1": [ + "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253" + ], + "2": [ + "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34" + ], + "mappings": [ + "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253" + ], + "samplesheet": [ + "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2" + ], + "versions": [ + "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34" + ] + } + ], + "timestamp": "2023-07-06T13:16:36+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test new file mode 100644 index 00000000..1558ff39 --- /dev/null +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -0,0 +1,31 @@ +nextflow_process { + + name "Test process: SRA_RUNINFO_TO_FTP" + script "modules/local/sra_runinfo_to_ftp/main.nf" + process "SRA_RUNINFO_TO_FTP" + tag "modules" + tag "modules_local" + tag "sra_runinfo_to_ftp" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap new file mode 100644 index 00000000..71a25f99 --- /dev/null +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" + ], + "1": [ + "versions.yml:md5,e95f8185f665127a73622a19d321bcca" + ], + "tsv": [ + "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" + ], + "versions": [ + "versions.yml:md5,e95f8185f665127a73622a19d321bcca" + ] + } + ], + "timestamp": "2023-08-06T23:13:20+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test new file mode 100644 index 00000000..b2ec5b11 --- /dev/null +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test process: SRA_TO_SAMPLESHEET" + script "modules/local/sra_to_samplesheet/main.nf" + process "SRA_TO_SAMPLESHEET" + tag "modules" + tag "modules_local" + tag "sra_to_samplesheet" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867', experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7', sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false] + input[1] = 'rnaseq' + input[2] = 'auto' + input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap new file mode 100644 index 00000000..e60c646a --- /dev/null +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -0,0 +1,113 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" + ] + ], + "1": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" + ] + ], + "mappings": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" + ] + ], + "samplesheet": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" + ] + ] + } + ], + "timestamp": "2023-08-23T09:38:15+0000" + } +} \ No newline at end of file From c95793e1e82b144ffb16ba8703e8072e80929aa5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 19:22:53 +0200 Subject: [PATCH 069/175] restore CI --- .github/workflows/ci.yml | 89 +++++++++++++++++++++++++++------------- 1 file changed, 61 insertions(+), 28 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 566ef509..7b7070e7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,28 +1,67 @@ +# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: pull_request: release: types: [published] + merge_group: + types: + - checks_requested + branches: + - master + - dev + - refactor env: NXF_ANSI_LOG: false + NFTEST_VER: "0.8.0-rc1" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true jobs: + changes: + name: Check for changes + runs-on: ubuntu-latest + outputs: + # Expose matched filters as job 'tags' output variable + tags: ${{ steps.filter.outputs.changes }} + steps: + - uses: actions/checkout@v3 + - uses: dorny/paths-filter@v2 + id: filter + with: + filters: ".github/tags.yml" + + define_nxf_versions: + name: Choose nextflow versions to test against depending on target branch + runs-on: ubuntu-latest + outputs: + matrix: ${{ steps.nxf_versions.outputs.matrix }} + steps: + - id: nxf_versions + run: | + if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT + else + echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT + fi + test: - name: Run pipeline with test data - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}" + name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} + needs: [changes, define_nxf_versions] + if: needs.changes.outputs.tags != '[]' runs-on: ubuntu-latest strategy: + fail-fast: false matrix: - NXF_VER: - - "23.04.0" - - "latest-everything" + NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} + tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] + profile: + - "docker" + steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -32,29 +71,23 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - name: Run pipeline with test data + - name: Install nf-test run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER + sudo mv nf-test /usr/local/bin/ - parameters: - name: Test workflow parameters - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }} - runs-on: ubuntu-latest - strategy: - matrix: - parameters: - - "--nf_core_pipeline rnaseq" - - "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout" - - "--skip_fastq_download" - - "--force_sratools_download" - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow + - name: Run nf-test run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with various parameters + nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml + + - name: Output log on failure + if: failure() run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} + sudo apt install bat > /dev/null + batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log + + - name: Publish Test Report + uses: mikepenz/action-junit-report@v3 + if: always() # always run even if the previous step fails + with: + report_paths: test.xml From 7e935bbbd1705853fd5f8858d9ca50dea4f466fa Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 19:26:37 +0200 Subject: [PATCH 070/175] forgot some files --- .gitattributes | 1 + .gitignore | 3 +++ nf-test.config | 16 ++++++++++++++++ 3 files changed, 20 insertions(+) create mode 100644 nf-test.config diff --git a/.gitattributes b/.gitattributes index 7a2dabc2..c1c17000 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,4 +1,5 @@ *.config linguist-language=nextflow *.nf.test linguist-language=nextflow +tests/**/*nf.test.snap linguist-generated modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated diff --git a/.gitignore b/.gitignore index 5124c9ac..b1b5890a 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,6 @@ results/ testing/ testing* *.pyc +.nf-test/ +nf-test +.nf-test.log diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..0799cb40 --- /dev/null +++ b/nf-test.config @@ -0,0 +1,16 @@ +config { + // location for all nf-tests + testsDir "." + + // nf-test directory including temporary files for each test + workDir ".nf-test" + + // location of library folder that is added automatically to the classpath + libDir "lib/" + + // location of an optional nextflow.config file specific for executing tests + configFile "nextflow.config" + + // run all test with the defined docker profile from the main nextflow.config + profile "" +} From e43e5f178e3812d000db3739f5f2c55a981e0e15 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 09:39:50 +0200 Subject: [PATCH 071/175] fix NXF_VER --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7b7070e7..59011a37 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,7 +46,7 @@ jobs: if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT else - echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT + echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT fi test: From eb11d0b2a54ea8b31411f3d5e5a9ca52bd833a81 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 22 Sep 2023 09:42:37 +0200 Subject: [PATCH 072/175] Delete .github/tags.yml this should happen in the `nf-test` branch --- .github/tags.yml | 79 ------------------------------------------------ 1 file changed, 79 deletions(-) delete mode 100644 .github/tags.yml diff --git a/.github/tags.yml b/.github/tags.yml deleted file mode 100644 index 9fc74a2c..00000000 --- a/.github/tags.yml +++ /dev/null @@ -1,79 +0,0 @@ -# local modules -multiqc_mappings_config: - - modules/local/multiqc_mappings_config/* -sra_fastq_ftp: - - modules/local/sra_fastq_ftp/* -sra_ids_to_runinfo: - - modules/local/sra_ids_to_runinfo/* -sra_merge_samplesheet: - - modules/local/sra_merge_samplesheet/* -sra_runinfo_to_ftp: - - modules/local/sra_runinfo_to_ftp/* -sra_to_samplesheet: - - modules/local/sra_to_samplesheet/* - -# workflow: sra -sra_custom_ena_metadata_fields: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* - - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test -sra_default_parameters: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* - - workflows/sra/tests/sra_default_parameters.nf.test -sra_force_sratools_download: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* - - workflows/sra/tests/sra_force_sratools_download.nf.test -sra_nf_core_pipeline_atacseq: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* - - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test -sra_nf_core_pipeline_rnaseq: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* - - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test -sra_nf_core_pipeline_taxprofiler: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* - - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test -sra_nf_core_pipeline_viralrecon: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* - - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test -sra_skip_fastq_download: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* - - workflows/sra/tests/sra_skip_fastq_download.nf.test From 185e930ca70cc3af853865b24af9f2ce893a1685 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 09:45:59 +0200 Subject: [PATCH 073/175] fix linting --- .nf-core.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.nf-core.yml b/.nf-core.yml index 9975ac5b..d617b3a3 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -6,3 +6,4 @@ lint: files_unchanged: - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy + - .gitattributes From 71e1a319dd342e7ecf5a810a9671e321cb9accce Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 22 Sep 2023 10:09:15 +0200 Subject: [PATCH 074/175] Delete conf/modules/base.config No need for this file anymore --- conf/modules/base.config | 33 --------------------------------- 1 file changed, 33 deletions(-) delete mode 100644 conf/modules/base.config diff --git a/conf/modules/base.config b/conf/modules/base.config deleted file mode 100644 index 035487c5..00000000 --- a/conf/modules/base.config +++ /dev/null @@ -1,33 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. ----------------------------------------------------------------------------------------- -*/ - -// -// Generic process options for all workflows -// -process { - - publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } - -} From 07b25b300fb424f8b7cebefd53edccfa8c42b0df Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 22 Sep 2023 10:10:58 +0200 Subject: [PATCH 075/175] Apply suggestions from code review --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 1e8bea6e..01da14f6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -162,7 +162,7 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } - test { includeConfig 'conf/test.config' } + test { includeConfig 'conf/test.config' } test_synapse { includeConfig 'conf/test_synapse.config' } test_full { includeConfig 'conf/test_full.config' } } From b11c1d8da1e0d68e5b80641690b3d0e5590990c1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 10:21:03 +0200 Subject: [PATCH 076/175] restore file --- .github/tags.yml | 71 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 .github/tags.yml diff --git a/.github/tags.yml b/.github/tags.yml new file mode 100644 index 00000000..a5914ccf --- /dev/null +++ b/.github/tags.yml @@ -0,0 +1,71 @@ +# local modules +multiqc_mappings_config: + - modules/local/multiqc_mappings_config/* +sra_fastq_ftp: + - modules/local/sra_fastq_ftp/* +sra_ids_to_runinfo: + - modules/local/sra_ids_to_runinfo/* +sra_merge_samplesheet: + - modules/local/sra_merge_samplesheet/* +sra_runinfo_to_ftp: + - modules/local/sra_runinfo_to_ftp/* +sra_to_samplesheet: + - modules/local/sra_to_samplesheet/* + +# workflow: sra +sra_custom_ena_metadata_fields: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_default_parameters: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_force_sratools_download: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_nf_core_pipeline_atacseq: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_nf_core_pipeline_rnaseq: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_nf_core_pipeline_taxprofiler: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_nf_core_pipeline_viralrecon: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_skip_fastq_download: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* From b0dd0a3c27a88371fa9ef5cdf6c42d334c845bb1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 10:23:07 +0200 Subject: [PATCH 077/175] do some tests --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 59011a37..5642602b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,6 +1,5 @@ # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors name: nf-core CI -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: pull_request: release: @@ -12,6 +11,7 @@ on: - master - dev - refactor + - nf-test env: NXF_ANSI_LOG: false From aad776b1166eeea52eeba789c9558233f4e7a4f7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 10:35:23 +0200 Subject: [PATCH 078/175] 2 * --- .github/tags.yml | 108 +++++++++++++++++++++++------------------------ 1 file changed, 54 insertions(+), 54 deletions(-) diff --git a/.github/tags.yml b/.github/tags.yml index a5914ccf..03569f78 100644 --- a/.github/tags.yml +++ b/.github/tags.yml @@ -1,71 +1,71 @@ # local modules multiqc_mappings_config: - - modules/local/multiqc_mappings_config/* + - modules/local/multiqc_mappings_config/** sra_fastq_ftp: - - modules/local/sra_fastq_ftp/* + - modules/local/sra_fastq_ftp/** sra_ids_to_runinfo: - - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_ids_to_runinfo/** sra_merge_samplesheet: - - modules/local/sra_merge_samplesheet/* + - modules/local/sra_merge_samplesheet/** sra_runinfo_to_ftp: - - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_runinfo_to_ftp/** sra_to_samplesheet: - - modules/local/sra_to_samplesheet/* + - modules/local/sra_to_samplesheet/** # workflow: sra sra_custom_ena_metadata_fields: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_default_parameters: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_force_sratools_download: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_nf_core_pipeline_atacseq: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_nf_core_pipeline_rnaseq: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_nf_core_pipeline_taxprofiler: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_nf_core_pipeline_viralrecon: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_skip_fastq_download: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** From 89d39e98727f7f0c8beb868b243f726a27a8bbd5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 10:49:40 +0200 Subject: [PATCH 079/175] forgot this file --- conf/test_data.config | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 conf/test_data.config diff --git a/conf/test_data.config b/conf/test_data.config new file mode 100644 index 00000000..42d3d818 --- /dev/null +++ b/conf/test_data.config @@ -0,0 +1,36 @@ +params { + // Base directory for test data + test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs" + + merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ] + + def merge_samplesheet_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/" + def merge_mappings_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/" + def merge_samplesheet_urls = [] + def merge_mappings_urls = [] + + merge_samplesheet_ids.each { id -> + merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv" + merge_mappings_urls += "${merge_mappings_url}/${id}.mappings.csv" + } + + fastq_ftp_ids = ["SRR13191702"] + def fastq_ftp_url = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/" + def fastq_ftp_urls = [] + + fastq_ftp_ids.each { id -> + fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz" + fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz" + } + + test_data { + 'modules_local' { + multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv" + sra_merge_samplesheet_samplesheets = merge_samplesheet_urls + sra_merge_samplesheet_mappings = merge_mappings_urls + sra_to_samplesheet = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv" + sra_fastq_ftp = fastq_ftp_urls + sra_runinfo_to_ftp = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv" + } + } +} From d456c208def2bf4e046b520ab9a72e91c27c0b2e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 11:00:43 +0200 Subject: [PATCH 080/175] fix path to file to include and update snapshots --- .../tests/main.nf.test.snap | 27 +------ .../sra_fastq_ftp/tests/main.nf.test.snap | 71 +------------------ .../tests/main.nf.test.snap | 2 +- .../tests/main.nf.test.snap | 2 +- .../tests/main.nf.test.snap | 2 +- .../tests/main.nf.test.snap | 2 +- nextflow.config | 5 +- 7 files changed, 10 insertions(+), 101 deletions(-) diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap index 9cf7fb38..1a4d16c4 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -1,29 +1,4 @@ { - "SRX9626017_SRR13191702": { - "content": [ - { - "0": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ], - "1": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "versions": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "yml": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ] - } - ], - "timestamp": "2023-08-17T12:02:35+0000" - }, "Should run without failures": { "content": [ { @@ -47,6 +22,6 @@ ] } ], - "timestamp": "2023-08-17T12:02:35+0000" + "timestamp": "2023-09-22T10:58:18.132284" } } \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap index c0d5ffdc..fb815455 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -1,73 +1,4 @@ { - "SRX9626017_SRR13191702": { - "content": [ - { - "0": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "1": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "2": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ], - "fastq": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "md5": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "versions": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ] - } - ], - "timestamp": "2023-08-06T23:31:57+0000" - }, "Should run without failures": { "content": [ { @@ -135,6 +66,6 @@ ] } ], - "timestamp": "2023-08-06T23:31:57+0000" + "timestamp": "2023-09-22T10:58:46.998421" } } \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap index dbca931f..241efe2a 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap @@ -16,6 +16,6 @@ ] } ], - "timestamp": "2023-08-06T23:30:51+0000" + "timestamp": "2023-09-22T10:58:56.721948" } } \ No newline at end of file diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap index c5f06aac..203395ae 100644 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap @@ -22,6 +22,6 @@ ] } ], - "timestamp": "2023-07-06T13:16:36+0000" + "timestamp": "2023-09-22T10:59:14.022116" } } \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap index 71a25f99..cd246303 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap @@ -16,6 +16,6 @@ ] } ], - "timestamp": "2023-08-06T23:13:20+0000" + "timestamp": "2023-09-22T10:58:36.16611" } } \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap index e60c646a..8cc8686a 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -108,6 +108,6 @@ ] } ], - "timestamp": "2023-08-23T09:38:15+0000" + "timestamp": "2023-09-22T10:58:27.169349" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 01da14f6..28fb66a0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -162,7 +162,10 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } - test { includeConfig 'conf/test.config' } + test { + includeConfig 'conf/test.config' + includeConfig 'conf/test_data.config' + } test_synapse { includeConfig 'conf/test_synapse.config' } test_full { includeConfig 'conf/test_full.config' } } From 938e7b99742aba5a285f77989ed839618a72f50b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 11:30:43 +0200 Subject: [PATCH 081/175] use initialise subworkflows --- main.nf | 22 +------- modules.json | 5 ++ subworkflows/nf-core/initialise/main.nf | 68 ++++++++++++++++++++++++ subworkflows/nf-core/initialise/meta.yml | 33 ++++++++++++ 4 files changed, 108 insertions(+), 20 deletions(-) create mode 100644 subworkflows/nf-core/initialise/main.nf create mode 100644 subworkflows/nf-core/initialise/meta.yml diff --git a/main.nf b/main.nf index 355898d0..a5011951 100644 --- a/main.nf +++ b/main.nf @@ -17,26 +17,6 @@ nextflow.enable.dsl = 2 ======================================================================================== */ -include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -// Print help message if needed -if (params.help) { - def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - // Check if --input file is empty ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } @@ -88,6 +68,7 @@ if (params.input_type == 'synapse') { include { MULTIQC_MAPPINGS_CONFIG } from './modules/local/multiqc_mappings_config' include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' +include { INITIALISE } from './subworkflows/nf-core/initialise/main' /* ======================================================================================== @@ -108,6 +89,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided // workflow NFCORE_FETCHNGS { + INITIALISE(params.version, params.help, params.valid_params) ch_versions = Channel.empty() diff --git a/modules.json b/modules.json index ab610dfb..46dc80ef 100644 --- a/modules.json +++ b/modules.json @@ -33,6 +33,11 @@ "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", "installed_by": ["subworkflows"] + }, + "initialise": { + "branch": "master", + "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475", + "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf new file mode 100644 index 00000000..0cbd3799 --- /dev/null +++ b/subworkflows/nf-core/initialise/main.nf @@ -0,0 +1,68 @@ +// This is a reimplementation of the basic initialise methods in the nf-core template +// The role of this subworkflow is to check the input parameters and print help messages +// Use this to start your nf-core pipeline + +include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation' + +workflow INITIALISE { + + take: + version // bool + help // bool + validate_params // bool + + main: + + // Print workflow version and exit on --version + if (version) { + String version_string = "" + + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + log.info "${workflow.manifest.name} ${version_string}" + System.exit(0) + } + + // Print citation for nf-core + def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " ${workflow.manifest.homePage}/blob/master/CITATIONS.md" + log.info citation + + // Print help message if needed + if (params.help) { + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker" + log.info paramsHelp(command) + System.exit(0) + } + + if ( params.validate_params != false ){ + validateParameters() + } + + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + } + + log.info paramsSummaryLog(workflow) + + summary_params = paramsSummaryMap(workflow) + + emit: + summary_params + +} diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml new file mode 100644 index 00000000..69596bb5 --- /dev/null +++ b/subworkflows/nf-core/initialise/meta.yml @@ -0,0 +1,33 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "initialise" +description: Validate input parameters and print help messages +keywords: + - admin + - check + - help + - version +modules: +input: + - version: + type: boolean + description: | + Structure: val(version) + Boolean to show the pipeline version and exit. + - help: + type: boolean + description: | + Structure: val(help) + Boolean to show the pipeline help message and exit. + - validate_params: + type: boolean + description: | + Structure: val(validate_params) + Whether to validate the parameters prior to starting the pipeline. +output: + - summary_params: + type: value + description: | + Structure: val(summary_params) + A map of the parameters used in the pipeline. +authors: + - "@adamrtalbot" From 8b8ed2f1642872c7abbaf86929d9d42f41e963f9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 09:42:52 +0200 Subject: [PATCH 082/175] code polish --- main.nf | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/main.nf b/main.nf index b7254a45..339eedd6 100644 --- a/main.nf +++ b/main.nf @@ -43,17 +43,24 @@ ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } // Read in ids from --input file -ch_ids = Channel.from(file(params.input, checkIfExists: true)) +Channel.from(file(params.input, checkIfExists: true)) .splitCsv(header:false, sep:'', strip:true) .map { it[0] } .unique() + .set { ch_ids } -// Auto-detect input type +// Auto-detect input id type def input_type = '' -if (WorkflowMain.isSraId(ch_input)) { input_type = 'sra' } -else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' } -else { error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') } -if (params.input_type != input_type) { error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") } +if (WorkflowMain.isSraId(ch_input)) { + input_type = 'sra' +} else if (WorkflowMain.isSynapseId(ch_input)) { + input_type = 'synapse' +} else { + error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') +} +if (params.input_type != input_type) { + error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") +} /* ======================================================================================== @@ -83,7 +90,7 @@ if (params.input_type == 'synapse') { /* ======================================================================================== - IMPORT MODULES + IMPORT MODULES/SUBWORKFLOWS ======================================================================================== */ From aa3339953f4e203730bcf4c47f794479e6ab7b07 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 09:57:09 +0200 Subject: [PATCH 083/175] more code polish --- main.nf | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 339eedd6..34f6d9ce 100644 --- a/main.nf +++ b/main.nf @@ -43,7 +43,8 @@ ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } // Read in ids from --input file -Channel.from(file(params.input, checkIfExists: true)) +Channel + .from(file(params.input, checkIfExists: true)) .splitCsv(header:false, sep:'', strip:true) .map { it[0] } .unique() @@ -75,9 +76,7 @@ if (params.input_type == 'sra') { // Validate input parameters WorkflowSra.initialise(params, valid_params) -} - -if (params.input_type == 'synapse') { +} else if (params.input_type == 'synapse') { // Create channel for synapse config if (params.synapse_config) { @@ -120,12 +119,16 @@ workflow NFCORE_FETCHNGS { ch_versions = Channel.empty() + // // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids + // if (params.input_type == 'sra') { SRA(ch_ids, params.sample_mapping_fields) ch_versions = ch_versions.mix(SRA.out.versions) + // // WORKFLOW: Download FastQ files for Synapse ids + // } else if (params.input_type == 'synapse') { SYNAPSE(ch_ids, ch_synapse_config) ch_versions = ch_versions.mix(SYNAPSE.out.versions) From 8ccf26a95c42c1dcbd2494be3ea1f4e1f2f0785e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:00:34 +0200 Subject: [PATCH 084/175] params --- main.nf | 2 +- workflows/sra/main.nf | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index 34f6d9ce..9617f85e 100644 --- a/main.nf +++ b/main.nf @@ -123,7 +123,7 @@ workflow NFCORE_FETCHNGS { // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids // if (params.input_type == 'sra') { - SRA(ch_ids, params.sample_mapping_fields) + SRA(ch_ids) ch_versions = ch_versions.mix(SRA.out.versions) // diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index e7e56b93..e92ae283 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -22,7 +22,6 @@ workflow SRA { take: ids // channel: [ ids ] - sample_mapping_fields main: ch_versions = Channel.empty() @@ -124,7 +123,7 @@ workflow SRA { ) ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) - if (sample_mapping_fields) { + if (params.sample_mapping_fields) { MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings) ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) } From 6f0189a6395f3d2cdb362fc5c8d9baf8c90044cd Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:27:52 +0200 Subject: [PATCH 085/175] more code polish --- lib/WorkflowMain.groovy | 111 +++++++++++++++++++++++++++++++++++++ lib/WorkflowSra.groovy | 33 ----------- lib/WorkflowSynapse.groovy | 92 ------------------------------ main.nf | 12 ++-- workflows/sra/main.nf | 14 +++-- workflows/synapse/main.nf | 6 +- 6 files changed, 128 insertions(+), 140 deletions(-) delete mode 100755 lib/WorkflowSra.groovy delete mode 100755 lib/WorkflowSynapse.groovy diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index f9469941..4ec4029a 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -102,4 +102,115 @@ class WorkflowMain { } return is_synapse } + + // + // Check and validate parameters + // + public static void sraInitialise(params, valid_params) { + // Check minimal ENA fields are provided to download FastQ files + def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields'] + if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) { + Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'") + } + } + + // + // Print a warning after pipeline has completed + // + public static void sraCurateSamplesheetWarn(log) { + log.warn "=============================================================================\n" + + " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + + " Public databases don't reliably hold information such as strandedness\n" + + " information, controls etc\n\n" + + " All of the sample metadata obtained from the ENA has been appended\n" + + " as additional columns to help you manually curate the samplesheet before\n" + + " running nf-core/other pipelines.\n" + + "===================================================================================" + } + + // + // Convert metadata obtained from the 'synapse show' command to a Groovy map + // + public static Map synapseShowToMap(synapse_file) { + def meta = [:] + def category = '' + synapse_file.eachLine { line -> + def entries = [null, null] + if (!line.startsWith(' ') && !line.trim().isEmpty()) { + category = line.tokenize(':')[0] + } else { + entries = line.trim().tokenize('=') + } + meta["${category}|${entries[0]}"] = entries[1] + } + meta.id = meta['properties|id'] + meta.name = meta['properties|name'] + meta.md5 = meta['File|md5'] + return meta.findAll{ it.value != null } + } + + // + // Print a warning after pipeline has completed + // + public static void synapseCurateSamplesheetWarn(log) { + log.warn "=============================================================================\n" + + " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + + " Where applicable, default values will be used for sample-specific metadata\n" + + " such as strandedness, controls etc as this information is not provided\n" + + " in a standardised manner when uploading data to Synapse.\n" + + "===================================================================================" + } + + // + // Obtain Sample ID from File Name + // + public static String synapseSampleNameFromFastQ(input_file, pattern) { + + def sampleids = "" + + def filePattern = pattern.toString() + int p = filePattern.lastIndexOf('/') + if( p != -1 ) + filePattern = filePattern.substring(p+1) + + input_file.each { + String fileName = input_file.getFileName().toString() + + String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' } + String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' } + if( indexOfWildcards==-1 && indexOfBrackets==-1 ) { + if( fileName == filePattern ) + return actual.getSimpleName() + throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName") + } + + int groupCount = 0 + for( int i=0; i - def entries = [null, null] - if (!line.startsWith(' ') && !line.trim().isEmpty()) { - category = line.tokenize(':')[0] - } else { - entries = line.trim().tokenize('=') - } - meta["${category}|${entries[0]}"] = entries[1] - } - meta.id = meta['properties|id'] - meta.name = meta['properties|name'] - meta.md5 = meta['File|md5'] - return meta.findAll{ it.value != null } - } - - // - // Print a warning after pipeline has completed - // - public static void curateSamplesheetWarn(log) { - log.warn "=============================================================================\n" + - " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + - " Where applicable, default values will be used for sample-specific metadata\n" + - " such as strandedness, controls etc as this information is not provided\n" + - " in a standardised manner when uploading data to Synapse.\n" + - "===================================================================================" - } - - // - // Obtain Sample ID from File Name - // - public static String sampleNameFromFastQ(input_file, pattern) { - - def sampleids = "" - - def filePattern = pattern.toString() - int p = filePattern.lastIndexOf('/') - if( p != -1 ) - filePattern = filePattern.substring(p+1) - - input_file.each { - String fileName = input_file.getFileName().toString() - - String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' } - String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' } - if( indexOfWildcards==-1 && indexOfBrackets==-1 ) { - if( fileName == filePattern ) - return actual.getSimpleName() - throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName") - } - - int groupCount = 0 - for( int i=0; i [ meta, [ meta.fastq_1, meta.fastq_2 ] ] @@ -69,6 +70,7 @@ workflow SRA { ftp: it[0].fastq_1 && !params.force_sratools_download sra: !it[0].fastq_1 || params.force_sratools_download } + .set { ch_sra_reads } // // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums @@ -88,12 +90,12 @@ workflow SRA { ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first()) // Isolate FASTQ channel which will be added to emit block - fastq_files = fastq_files.mix( + fastq_files.mix( SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads - ) + ).set { fastq_files } - ch_sra_metadata = fastq_files.map { meta, fastq -> + fastq_files.map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() @@ -101,7 +103,7 @@ workflow SRA { meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : '' return meta_clone - } + }.set { ch_sra_metadata } } // diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 30d05f4f..785877ac 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -56,7 +56,7 @@ workflow SYNAPSE { SYNAPSE_SHOW .out .metadata - .map { it -> WorkflowSynapse.synapseShowToMap(it) } + .map { it -> Workflow.synapseShowToMap(it) } .set { ch_samples_meta } // @@ -72,14 +72,14 @@ workflow SYNAPSE { SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } + .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } .groupTuple(sort: { it -> it.baseName }) .set { ch_fastq } SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } + .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } .groupTuple() .join(ch_fastq) .map { id, synids, fastq -> From 37229aba32279f5fcb1107215847431362b7bdb6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:32:24 +0200 Subject: [PATCH 086/175] typo --- main.nf | 8 ++++---- workflows/synapse/main.nf | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/main.nf b/main.nf index f0f40588..95cc5fbc 100644 --- a/main.nf +++ b/main.nf @@ -28,7 +28,7 @@ log.info logo + paramsSummaryLog(workflow) + citation // Print help message if needed if (params.help) { - def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker" + def String command = "nextflow run ${WorkflowMain.manifest.name} --input id.csv -profile docker" log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) System.exit(0) } @@ -75,7 +75,7 @@ if (params.input_type == 'sra') { ] // Validate input parameters - Workflow.sraInitialise(params, valid_params) + WorkflowMain.sraInitialise(params, valid_params) } else if (params.input_type == 'synapse') { // Create channel for synapse config @@ -163,8 +163,8 @@ workflow.onComplete { NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) } NfcoreTemplate.summary(workflow, params, log) - if (params.input_type == 'sra') { Workflow.sraCurateSamplesheetWarn(log) } - if (params.input_type == 'synapse') { Workflow.synapseCurateSamplesheetWarn(log) } + if (params.input_type == 'sra') { WorkflowMain.sraCurateSamplesheetWarn(log) } + if (params.input_type == 'synapse') { WorkflowMain.synapseCurateSamplesheetWarn(log) } } /* diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 785877ac..0fc46ed4 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -56,7 +56,7 @@ workflow SYNAPSE { SYNAPSE_SHOW .out .metadata - .map { it -> Workflow.synapseShowToMap(it) } + .map { it -> WorkflowMain.synapseShowToMap(it) } .set { ch_samples_meta } // @@ -72,14 +72,14 @@ workflow SYNAPSE { SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } + .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } .groupTuple(sort: { it -> it.baseName }) .set { ch_fastq } SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } + .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } .groupTuple() .join(ch_fastq) .map { id, synids, fastq -> From ef3a5cfd3ee6f093ed99b5e535e0d94c747b0c46 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 25 Sep 2023 10:45:28 +0200 Subject: [PATCH 087/175] Apply suggestions from code review --- main.nf | 2 +- workflows/sra/main.nf | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index 95cc5fbc..70e8ff27 100644 --- a/main.nf +++ b/main.nf @@ -28,7 +28,7 @@ log.info logo + paramsSummaryLog(workflow) + citation // Print help message if needed if (params.help) { - def String command = "nextflow run ${WorkflowMain.manifest.name} --input id.csv -profile docker" + def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker" log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) System.exit(0) } diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index d59b1908..45efa9c9 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -53,7 +53,7 @@ workflow SRA { return meta_clone } .unique() - .set{ ch_sra_metadata } + .set { ch_sra_metadata } ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first()) @@ -93,9 +93,7 @@ workflow SRA { fastq_files.mix( SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads - ).set { fastq_files } - - fastq_files.map { meta, fastq -> + ).map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() @@ -126,7 +124,9 @@ workflow SRA { ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) if (params.sample_mapping_fields) { - MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings) + MULTIQC_MAPPINGS_CONFIG ( + SRA_MERGE_SAMPLESHEET.out.mappings + ) ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) } From cdaf06fa7150f2f994d9214d132f3e83b9e141b5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 11:30:43 +0200 Subject: [PATCH 088/175] use initialise subworkflows --- main.nf | 22 +------- modules.json | 5 ++ subworkflows/nf-core/initialise/main.nf | 68 ++++++++++++++++++++++++ subworkflows/nf-core/initialise/meta.yml | 33 ++++++++++++ 4 files changed, 108 insertions(+), 20 deletions(-) create mode 100644 subworkflows/nf-core/initialise/main.nf create mode 100644 subworkflows/nf-core/initialise/meta.yml diff --git a/main.nf b/main.nf index 355898d0..a5011951 100644 --- a/main.nf +++ b/main.nf @@ -17,26 +17,6 @@ nextflow.enable.dsl = 2 ======================================================================================== */ -include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -// Print help message if needed -if (params.help) { - def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - // Check if --input file is empty ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } @@ -88,6 +68,7 @@ if (params.input_type == 'synapse') { include { MULTIQC_MAPPINGS_CONFIG } from './modules/local/multiqc_mappings_config' include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' +include { INITIALISE } from './subworkflows/nf-core/initialise/main' /* ======================================================================================== @@ -108,6 +89,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided // workflow NFCORE_FETCHNGS { + INITIALISE(params.version, params.help, params.valid_params) ch_versions = Channel.empty() diff --git a/modules.json b/modules.json index ab610dfb..46dc80ef 100644 --- a/modules.json +++ b/modules.json @@ -33,6 +33,11 @@ "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", "installed_by": ["subworkflows"] + }, + "initialise": { + "branch": "master", + "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475", + "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf new file mode 100644 index 00000000..0cbd3799 --- /dev/null +++ b/subworkflows/nf-core/initialise/main.nf @@ -0,0 +1,68 @@ +// This is a reimplementation of the basic initialise methods in the nf-core template +// The role of this subworkflow is to check the input parameters and print help messages +// Use this to start your nf-core pipeline + +include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation' + +workflow INITIALISE { + + take: + version // bool + help // bool + validate_params // bool + + main: + + // Print workflow version and exit on --version + if (version) { + String version_string = "" + + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + log.info "${workflow.manifest.name} ${version_string}" + System.exit(0) + } + + // Print citation for nf-core + def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " ${workflow.manifest.homePage}/blob/master/CITATIONS.md" + log.info citation + + // Print help message if needed + if (params.help) { + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker" + log.info paramsHelp(command) + System.exit(0) + } + + if ( params.validate_params != false ){ + validateParameters() + } + + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + } + + log.info paramsSummaryLog(workflow) + + summary_params = paramsSummaryMap(workflow) + + emit: + summary_params + +} diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml new file mode 100644 index 00000000..69596bb5 --- /dev/null +++ b/subworkflows/nf-core/initialise/meta.yml @@ -0,0 +1,33 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "initialise" +description: Validate input parameters and print help messages +keywords: + - admin + - check + - help + - version +modules: +input: + - version: + type: boolean + description: | + Structure: val(version) + Boolean to show the pipeline version and exit. + - help: + type: boolean + description: | + Structure: val(help) + Boolean to show the pipeline help message and exit. + - validate_params: + type: boolean + description: | + Structure: val(validate_params) + Whether to validate the parameters prior to starting the pipeline. +output: + - summary_params: + type: value + description: | + Structure: val(summary_params) + A map of the parameters used in the pipeline. +authors: + - "@adamrtalbot" From b8b15903aa71378d9357ab61c7e3c2f93a9d4d51 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 12:00:32 +0200 Subject: [PATCH 089/175] move scripts --- workflows/sra/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 8d5149d2..8b5f649e 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -9,6 +9,7 @@ include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp' include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet' +include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config' /* ======================================================================================== From b6c71a112e971d918c048bc4899dbfe131dab923 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 17:59:55 +0200 Subject: [PATCH 090/175] no need to test on push on dev, pr are enough --- .nf-core.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.nf-core.yml b/.nf-core.yml index d617b3a3..78f1faff 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,7 +2,11 @@ repository_type: pipeline lint: actions_ci: false files_exist: + - .github/workflows/awsfulltest.yml + - .github/workflows/awstest.yml + - conf/igenomes.config - conf/modules.config + - lib/WorkflowFetchngs.groovy files_unchanged: - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy From d6f8971a23c7432cc8a5655340ba627323b2410e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 18:08:35 +0200 Subject: [PATCH 091/175] more code polish --- main.nf | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/main.nf b/main.nf index a5011951..aa24ed36 100644 --- a/main.nf +++ b/main.nf @@ -1,4 +1,5 @@ #!/usr/bin/env nextflow + /* ======================================================================================== nf-core/fetchngs @@ -66,7 +67,6 @@ if (params.input_type == 'synapse') { ======================================================================================== */ -include { MULTIQC_MAPPINGS_CONFIG } from './modules/local/multiqc_mappings_config' include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' include { INITIALISE } from './subworkflows/nf-core/initialise/main' @@ -98,12 +98,6 @@ workflow NFCORE_FETCHNGS { SRA(ch_ids) ch_versions = ch_versions.mix(SRA.out.versions) - // MODULE: Create a MultiQC config file with sample name mappings - if (params.sample_mapping_fields) { - MULTIQC_MAPPINGS_CONFIG(SRA.out.mappings) - ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) - } - // WORKFLOW: Download FastQ files for Synapse ids } else if (params.input_type == 'synapse') { SYNAPSE(ch_ids, ch_synapse_config) @@ -115,9 +109,9 @@ workflow NFCORE_FETCHNGS { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== RUN ALL WORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ // From a968fcb29bb5791199f921f2823f7f6c848539e3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 09:42:52 +0200 Subject: [PATCH 092/175] code polish --- main.nf | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/main.nf b/main.nf index aa24ed36..a67acf26 100644 --- a/main.nf +++ b/main.nf @@ -23,17 +23,24 @@ ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } // Read in ids from --input file -ch_ids = Channel.from(file(params.input, checkIfExists: true)) +Channel.from(file(params.input, checkIfExists: true)) .splitCsv(header:false, sep:'', strip:true) .map { it[0] } .unique() + .set { ch_ids } -// Auto-detect input type +// Auto-detect input id type def input_type = '' -if (WorkflowMain.isSraId(ch_input)) { input_type = 'sra' } -else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' } -else { error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') } -if (params.input_type != input_type) { error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") } +if (WorkflowMain.isSraId(ch_input)) { + input_type = 'sra' +} else if (WorkflowMain.isSynapseId(ch_input)) { + input_type = 'synapse' +} else { + error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') +} +if (params.input_type != input_type) { + error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") +} /* ======================================================================================== @@ -63,7 +70,7 @@ if (params.input_type == 'synapse') { /* ======================================================================================== - IMPORT MODULES + IMPORT MODULES/SUBWORKFLOWS ======================================================================================== */ From 58f92b086478fabcb1a106678c34e15f42a6e40d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 09:57:09 +0200 Subject: [PATCH 093/175] more code polish --- main.nf | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index a67acf26..22977145 100644 --- a/main.nf +++ b/main.nf @@ -23,7 +23,8 @@ ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } // Read in ids from --input file -Channel.from(file(params.input, checkIfExists: true)) +Channel + .from(file(params.input, checkIfExists: true)) .splitCsv(header:false, sep:'', strip:true) .map { it[0] } .unique() @@ -55,9 +56,7 @@ if (params.input_type == 'sra') { // Validate input parameters WorkflowSra.initialise(params, valid_params) -} - -if (params.input_type == 'synapse') { +} else if (params.input_type == 'synapse') { // Create channel for synapse config if (params.synapse_config) { @@ -100,12 +99,16 @@ workflow NFCORE_FETCHNGS { ch_versions = Channel.empty() + // // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids + // if (params.input_type == 'sra') { SRA(ch_ids) ch_versions = ch_versions.mix(SRA.out.versions) + // // WORKFLOW: Download FastQ files for Synapse ids + // } else if (params.input_type == 'synapse') { SYNAPSE(ch_ids, ch_synapse_config) ch_versions = ch_versions.mix(SYNAPSE.out.versions) From c98917663793ea5af43afcf85d8b75a7f83e16af Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:00:34 +0200 Subject: [PATCH 094/175] params --- workflows/sra/main.nf | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 8b5f649e..de3eaf8b 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -130,6 +130,11 @@ workflow SRA { ) ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) + if (params.sample_mapping_fields) { + MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings) + ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) + } + emit: fastq = fastq_files samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet From 131fd1b6fa42679d8cd779039e8f40de333d4e95 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:27:52 +0200 Subject: [PATCH 095/175] more code polish --- lib/WorkflowMain.groovy | 111 +++++++++++++++++++++++++++++++++++++ lib/WorkflowSra.groovy | 33 ----------- lib/WorkflowSynapse.groovy | 92 ------------------------------ main.nf | 12 ++-- workflows/sra/main.nf | 14 +++-- workflows/synapse/main.nf | 6 +- 6 files changed, 128 insertions(+), 140 deletions(-) delete mode 100755 lib/WorkflowSra.groovy delete mode 100755 lib/WorkflowSynapse.groovy diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index f9469941..4ec4029a 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -102,4 +102,115 @@ class WorkflowMain { } return is_synapse } + + // + // Check and validate parameters + // + public static void sraInitialise(params, valid_params) { + // Check minimal ENA fields are provided to download FastQ files + def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields'] + if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) { + Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'") + } + } + + // + // Print a warning after pipeline has completed + // + public static void sraCurateSamplesheetWarn(log) { + log.warn "=============================================================================\n" + + " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + + " Public databases don't reliably hold information such as strandedness\n" + + " information, controls etc\n\n" + + " All of the sample metadata obtained from the ENA has been appended\n" + + " as additional columns to help you manually curate the samplesheet before\n" + + " running nf-core/other pipelines.\n" + + "===================================================================================" + } + + // + // Convert metadata obtained from the 'synapse show' command to a Groovy map + // + public static Map synapseShowToMap(synapse_file) { + def meta = [:] + def category = '' + synapse_file.eachLine { line -> + def entries = [null, null] + if (!line.startsWith(' ') && !line.trim().isEmpty()) { + category = line.tokenize(':')[0] + } else { + entries = line.trim().tokenize('=') + } + meta["${category}|${entries[0]}"] = entries[1] + } + meta.id = meta['properties|id'] + meta.name = meta['properties|name'] + meta.md5 = meta['File|md5'] + return meta.findAll{ it.value != null } + } + + // + // Print a warning after pipeline has completed + // + public static void synapseCurateSamplesheetWarn(log) { + log.warn "=============================================================================\n" + + " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + + " Where applicable, default values will be used for sample-specific metadata\n" + + " such as strandedness, controls etc as this information is not provided\n" + + " in a standardised manner when uploading data to Synapse.\n" + + "===================================================================================" + } + + // + // Obtain Sample ID from File Name + // + public static String synapseSampleNameFromFastQ(input_file, pattern) { + + def sampleids = "" + + def filePattern = pattern.toString() + int p = filePattern.lastIndexOf('/') + if( p != -1 ) + filePattern = filePattern.substring(p+1) + + input_file.each { + String fileName = input_file.getFileName().toString() + + String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' } + String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' } + if( indexOfWildcards==-1 && indexOfBrackets==-1 ) { + if( fileName == filePattern ) + return actual.getSimpleName() + throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName") + } + + int groupCount = 0 + for( int i=0; i - def entries = [null, null] - if (!line.startsWith(' ') && !line.trim().isEmpty()) { - category = line.tokenize(':')[0] - } else { - entries = line.trim().tokenize('=') - } - meta["${category}|${entries[0]}"] = entries[1] - } - meta.id = meta['properties|id'] - meta.name = meta['properties|name'] - meta.md5 = meta['File|md5'] - return meta.findAll{ it.value != null } - } - - // - // Print a warning after pipeline has completed - // - public static void curateSamplesheetWarn(log) { - log.warn "=============================================================================\n" + - " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + - " Where applicable, default values will be used for sample-specific metadata\n" + - " such as strandedness, controls etc as this information is not provided\n" + - " in a standardised manner when uploading data to Synapse.\n" + - "===================================================================================" - } - - // - // Obtain Sample ID from File Name - // - public static String sampleNameFromFastQ(input_file, pattern) { - - def sampleids = "" - - def filePattern = pattern.toString() - int p = filePattern.lastIndexOf('/') - if( p != -1 ) - filePattern = filePattern.substring(p+1) - - input_file.each { - String fileName = input_file.getFileName().toString() - - String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' } - String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' } - if( indexOfWildcards==-1 && indexOfBrackets==-1 ) { - if( fileName == filePattern ) - return actual.getSimpleName() - throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName") - } - - int groupCount = 0 - for( int i=0; i [ meta, [ meta.fastq_1, meta.fastq_2 ] ] @@ -76,6 +77,7 @@ workflow SRA { ftp: it[0].fastq_1 && !params.force_sratools_download sra: !it[0].fastq_1 || params.force_sratools_download } + .set { ch_sra_reads } // // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums @@ -95,12 +97,12 @@ workflow SRA { ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first()) // Isolate FASTQ channel which will be added to emit block - fastq_files = fastq_files.mix( + fastq_files.mix( SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads - ) + ).set { fastq_files } - ch_sra_metadata = fastq_files.map { meta, fastq -> + fastq_files.map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() @@ -108,7 +110,7 @@ workflow SRA { meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : '' return meta_clone - } + }.set { ch_sra_metadata } } // diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 30d05f4f..785877ac 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -56,7 +56,7 @@ workflow SYNAPSE { SYNAPSE_SHOW .out .metadata - .map { it -> WorkflowSynapse.synapseShowToMap(it) } + .map { it -> Workflow.synapseShowToMap(it) } .set { ch_samples_meta } // @@ -72,14 +72,14 @@ workflow SYNAPSE { SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } + .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } .groupTuple(sort: { it -> it.baseName }) .set { ch_fastq } SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } + .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } .groupTuple() .join(ch_fastq) .map { id, synids, fastq -> From 08d30eb30dad60108b780517a2bb70540b1090d8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:32:24 +0200 Subject: [PATCH 096/175] typo --- main.nf | 6 +++--- workflows/synapse/main.nf | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index 91aa6601..d74b62f8 100644 --- a/main.nf +++ b/main.nf @@ -55,7 +55,7 @@ if (params.input_type == 'sra') { ] // Validate input parameters - Workflow.sraInitialise(params, valid_params) + WorkflowMain.sraInitialise(params, valid_params) } else if (params.input_type == 'synapse') { // Create channel for synapse config @@ -143,8 +143,8 @@ workflow.onComplete { NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) } NfcoreTemplate.summary(workflow, params, log) - if (params.input_type == 'sra') { Workflow.sraCurateSamplesheetWarn(log) } - if (params.input_type == 'synapse') { Workflow.synapseCurateSamplesheetWarn(log) } + if (params.input_type == 'sra') { WorkflowMain.sraCurateSamplesheetWarn(log) } + if (params.input_type == 'synapse') { WorkflowMain.synapseCurateSamplesheetWarn(log) } } /* diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 785877ac..0fc46ed4 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -56,7 +56,7 @@ workflow SYNAPSE { SYNAPSE_SHOW .out .metadata - .map { it -> Workflow.synapseShowToMap(it) } + .map { it -> WorkflowMain.synapseShowToMap(it) } .set { ch_samples_meta } // @@ -72,14 +72,14 @@ workflow SYNAPSE { SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } + .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } .groupTuple(sort: { it -> it.baseName }) .set { ch_fastq } SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } + .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } .groupTuple() .join(ch_fastq) .map { id, synids, fastq -> From 034a52023931d1bcdd07cef94e1bff8fa1e2b0fe Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 11:11:07 +0200 Subject: [PATCH 097/175] use rc2 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5642602b..30656e1a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.0-rc1" + NFTEST_VER: "0.8.0-rc2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From 45c9020c2d24e669ed2f9b8a5e30dbb56018bc51 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 11:11:25 +0200 Subject: [PATCH 098/175] regenerate tests and snapshots --- .../sra_custom_ena_metadata_fields.nf.test | 2 +- ...ra_custom_ena_metadata_fields.nf.test.snap | 62 ++-------- .../sra/tests/sra_default_parameters.nf.test | 2 +- .../tests/sra_default_parameters.nf.test.snap | 114 ++---------------- .../tests/sra_force_sratools_download.nf.test | 2 +- .../sra_force_sratools_download.nf.test.snap | 110 ++--------------- .../sra_nf_core_pipeline_atacseq.nf.test | 2 +- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 114 ++---------------- .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 114 ++---------------- .../sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 114 ++---------------- .../sra_nf_core_pipeline_viralrecon.nf.test | 2 +- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 114 ++---------------- .../sra/tests/sra_skip_fastq_download.nf.test | 2 +- .../sra_skip_fastq_download.nf.test.snap | 20 +-- 16 files changed, 108 insertions(+), 670 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 45280ab0..7c9df9d9 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index a2537a95..29feb896 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -38,25 +38,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "library_layout": "PAIRED", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -272,17 +253,18 @@ ] ], "1": [ - "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562" + "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5" ], "2": [ - "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f" + "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" ], "3": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -320,25 +302,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "library_layout": "PAIRED", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -554,20 +517,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f" + "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" ], "samplesheet": [ - "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562" + "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5" ], "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:48:18.757655" + "timestamp": "2023-09-25T10:51:46.450639" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_default_parameters.nf.test b/workflows/sra/tests/sra_default_parameters.nf.test index ef35c80a..b525bec5 100644 --- a/workflows/sra/tests/sra_default_parameters.nf.test +++ b/workflows/sra/tests/sra_default_parameters.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap index b8dc88ca..ea2b868a 100644 --- a/workflows/sra/tests/sra_default_parameters.nf.test.snap +++ b/workflows/sra/tests/sra_default_parameters.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:56:05.693225" + "timestamp": "2023-09-25T10:59:42.069791" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 76ce7cd3..2548689d 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 4e1b8aaf..7fdbbf66 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22", - "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,16 +617,17 @@ ] ], "1": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ [ @@ -761,51 +717,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22", - "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1333,19 +1244,20 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-09-11T19:02:05.556134" + "timestamp": "2023-09-25T11:09:38.27192" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 0ce0c230..ad60725c 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index f6528e52..0cbec631 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c" + "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c" + "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:37:54.607231" + "timestamp": "2023-09-25T10:45:48.713699" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 67c0fbe4..993590ff 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 124877ae..c6bd2d32 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80" + "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80" + "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767" ], "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:51:38.198125" + "timestamp": "2023-09-25T11:02:54.001279" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index e00793cd..a5e69da1 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index b63ad4b7..4d57827d 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c" + "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c" + "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc" ], "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:44:02.293186" + "timestamp": "2023-09-25T10:48:46.519896" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 045e0363..f64cf92e 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 1387f422..3520d5bf 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:34:25.049818" + "timestamp": "2023-09-25T10:42:52.035768" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 67abee3b..aa290c68 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index 3b04b917..91a10c87 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -6,32 +6,34 @@ ], "1": [ - "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-09-11T18:56:34.175665" + "timestamp": "2023-09-25T11:03:28.968158" } } \ No newline at end of file From 191a8e724285471f8d698ce15eebac3fbdeeb95f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 25 Sep 2023 10:45:28 +0200 Subject: [PATCH 099/175] Apply suggestions from code review --- workflows/sra/main.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 46a2c809..43beb51d 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -60,7 +60,7 @@ workflow SRA { return meta_clone } .unique() - .set{ ch_sra_metadata } + .set { ch_sra_metadata } ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first()) @@ -100,9 +100,7 @@ workflow SRA { fastq_files.mix( SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads - ).set { fastq_files } - - fastq_files.map { meta, fastq -> + ).map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() @@ -133,7 +131,9 @@ workflow SRA { ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) if (params.sample_mapping_fields) { - MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings) + MULTIQC_MAPPINGS_CONFIG ( + SRA_MERGE_SAMPLESHEET.out.mappings + ) ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) } From e4fddb4901c935c11fac01ab0efddc5755555be7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 11:46:06 +0200 Subject: [PATCH 100/175] final code polish --- main.nf | 20 -------------------- workflows/sra/main.nf | 21 ++++++++++++++------- 2 files changed, 14 insertions(+), 27 deletions(-) diff --git a/main.nf b/main.nf index 70e8ff27..d74b62f8 100644 --- a/main.nf +++ b/main.nf @@ -18,26 +18,6 @@ nextflow.enable.dsl = 2 ======================================================================================== */ -include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -// Print help message if needed -if (params.help) { - def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - // Check if --input file is empty ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 45efa9c9..920579d1 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -1,15 +1,22 @@ /* ======================================================================================== - IMPORT LOCAL MODULES/SUBWORKFLOWS + IMPORT LOCAL MODULES +======================================================================================== +*/ + +include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config' +include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp' +include { SRA_IDS_TO_RUNINFO } from '../../modules/local/sra_ids_to_runinfo' +include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet' +include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp' +include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' + +/* +======================================================================================== + IMPORT NF-CORE SUBWORKFLOWS ======================================================================================== */ -include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config' -include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp' -include { SRA_IDS_TO_RUNINFO } from '../../modules/local/sra_ids_to_runinfo' -include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet' -include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp' -include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools' /* From 9b850ba02896b4753c7a3c9921616f70a611269c Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 25 Sep 2023 12:11:13 +0200 Subject: [PATCH 101/175] Apply suggestions from code review --- main.nf | 4 +++- workflows/sra/main.nf | 3 +++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/main.nf b/main.nf index d74b62f8..c6d7d13e 100644 --- a/main.nf +++ b/main.nf @@ -115,7 +115,9 @@ workflow NFCORE_FETCHNGS { } // MODULE: Dump software versions for all tools used in the workflow - CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml')) + // + // MODULE: Dump software versions for all tools used in the workflow + // } /* diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 920579d1..2b221739 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -130,6 +130,9 @@ workflow SRA { ) ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) + // + // MODULE: Create a MutiQC config file with sample name mappings + // if (params.sample_mapping_fields) { MULTIQC_MAPPINGS_CONFIG ( SRA_MERGE_SAMPLESHEET.out.mappings From 6cf3085c08ab4654cba21ac3bdfccd6d3e7745b5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 12:12:16 +0200 Subject: [PATCH 102/175] update snapshots --- ...ra_custom_ena_metadata_fields.nf.test.snap | 500 +------ .../tests/sra_default_parameters.nf.test.snap | 1228 +---------------- .../sra_force_sratools_download.nf.test.snap | 1228 +---------------- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 1228 +---------------- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 1228 +---------------- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 1228 +---------------- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 1228 +---------------- 7 files changed, 21 insertions(+), 7847 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 29feb896..7a7df129 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -3,254 +3,7 @@ "content": [ { "0": [ - 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"fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz", - "md5_1": "795d460abff6009c7f5ff7c14b773fbe", - "md5_2": "c3f34379356b28d6dac7212abc1a0a04", - "single_end": false - }, - [ - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04" - ] - ], - [ - { - "id": "SRX9626017_SRR13191702", - "run_accession": "SRR13191702", - "experiment_accession": "SRX9626017", - "sample_accession": "SAMN16980141", - "secondary_sample_accession": "SRS7827211", - "study_accession": "PRJNA682076", - "secondary_study_accession": "SRP295653", - "submission_accession": "SRA1166126", - "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz", - "experiment_alias": "S.170804.00784", - "sample_alias": "S.170804.00784_662", - "study_alias": "PRJNA682076", - "library_layout": "PAIRED", - "library_selection": "PCR", - "library_source": "METAGENOMIC", - "library_strategy": "AMPLICON", - "library_name": "S.170804.00784", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "45682", - "read_count": "91", - "tax_id": "408170", - "scientific_name": "human gut metagenome", - "sample_title": "Metagenome or environmental sample from human gut metagenome", - "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", - "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", - "sample_description": "Metagenome or environmental sample from human gut metagenome", - "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98", - "fastq_bytes": "15420;16324", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98", - "single_end": false - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] + ], "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" @@ -1260,6 +38,6 @@ ] } ], - "timestamp": "2023-09-25T10:42:52.035768" + "timestamp": "2023-09-25T11:50:52.373496" } } \ No newline at end of file From 67ffe73a4eb1270983542fef47823037f2636834 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 25 Sep 2023 12:32:06 +0200 Subject: [PATCH 103/175] Update main.nf --- main.nf | 5 ----- 1 file changed, 5 deletions(-) diff --git a/main.nf b/main.nf index c6d7d13e..2733a41a 100644 --- a/main.nf +++ b/main.nf @@ -113,11 +113,6 @@ workflow NFCORE_FETCHNGS { SYNAPSE ( ch_ids, ch_synapse_config ) ch_versions = ch_versions.mix(SYNAPSE.out.versions) } - - // MODULE: Dump software versions for all tools used in the workflow - // - // MODULE: Dump software versions for all tools used in the workflow - // } /* From 8114abc1c23c92fc1021fb79dfc27e79b01a3fbc Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 6 Oct 2023 11:47:54 +0200 Subject: [PATCH 104/175] Update main.nf --- workflows/sra/main.nf | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 441430ea..562d1726 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -133,18 +133,21 @@ workflow SRA { // // MODULE: Create a MutiQC config file with sample name mappings // + ch_sample_mappings_yml = Channel.empty() if (params.sample_mapping_fields) { MULTIQC_MAPPINGS_CONFIG ( SRA_MERGE_SAMPLESHEET.out.mappings ) ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) + ch_sample_mappings_yml = MULTIQC_MAPPINGS_CONFIG.out.yml } emit: - fastq = fastq_files - samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet - mappings = SRA_MERGE_SAMPLESHEET.out.mappings - versions = ch_versions.unique() + fastq = fastq_files + samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet + mappings = SRA_MERGE_SAMPLESHEET.out.mappings + sample_mappings = ch_sample_mappings_yml + versions = ch_versions.unique() } /* From 56e5143fbf3d14b944183df461e5c0903ac7faea Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 6 Oct 2023 12:25:48 +0200 Subject: [PATCH 105/175] update snapshots --- .github/workflows/ci.yml | 2 +- ...sra_default_parameters.nf.test => main.nf.test} | 0 ...t_parameters.nf.test.snap => main.nf.test.snap} | 14 +++++++++++++- .../sra_custom_ena_metadata_fields.nf.test.snap | 14 +++++++++++++- .../tests/sra_force_sratools_download.nf.test.snap | 14 +++++++++++++- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 14 +++++++++++++- .../tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 14 +++++++++++++- .../sra_nf_core_pipeline_taxprofiler.nf.test.snap | 14 +++++++++++++- .../sra_nf_core_pipeline_viralrecon.nf.test.snap | 14 +++++++++++++- .../sra/tests/sra_skip_fastq_download.nf.test.snap | 14 +++++++++++++- 10 files changed, 105 insertions(+), 9 deletions(-) rename workflows/sra/tests/{sra_default_parameters.nf.test => main.nf.test} (100%) rename workflows/sra/tests/{sra_default_parameters.nf.test.snap => main.nf.test.snap} (75%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 30656e1a..68e2773c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.0-rc2" + NFTEST_VER: "0.8.0" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" diff --git a/workflows/sra/tests/sra_default_parameters.nf.test b/workflows/sra/tests/main.nf.test similarity index 100% rename from workflows/sra/tests/sra_default_parameters.nf.test rename to workflows/sra/tests/main.nf.test diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/main.nf.test.snap similarity index 75% rename from workflows/sra/tests/sra_default_parameters.nf.test.snap rename to workflows/sra/tests/main.nf.test.snap index edb662a2..955dd72a 100644 --- a/workflows/sra/tests/sra_default_parameters.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T12:00:37.501679" + "timestamp": "2023-10-06T12:18:32.149462" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 7a7df129..143375ac 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" ], "3": [ + [ + "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T11:58:11.85816" + "timestamp": "2023-10-06T12:10:32.762201" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 91eec432..5cb1876c 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -24,6 +30,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], @@ -36,6 +48,6 @@ ] } ], - "timestamp": "2023-09-25T12:08:28.465466" + "timestamp": "2023-10-06T12:24:57.695874" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 4560b05b..60cd3444 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T11:53:25.411769" + "timestamp": "2023-10-06T12:03:19.401141" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 26357aa5..a0c20a40 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T12:03:02.485911" + "timestamp": "2023-10-06T12:14:02.500312" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index ff4b27df..d9d6ddee 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T11:55:48.759498" + "timestamp": "2023-10-06T12:07:01.184728" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 4b38d6a1..c3e9ae8b 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T11:50:52.373496" + "timestamp": "2023-10-06T11:59:31.7356" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index 91a10c87..c137d853 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", @@ -23,6 +29,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b" ], @@ -34,6 +46,6 @@ ] } ], - "timestamp": "2023-09-25T11:03:28.968158" + "timestamp": "2023-10-06T12:18:48.477246" } } \ No newline at end of file From f689be7aa466dfdd4842ce5ffcd841fa6c5109cc Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sun, 8 Oct 2023 16:47:06 +0100 Subject: [PATCH 106/175] Bump pipeline version to 1.11.0dev --- CHANGELOG.md | 4 ++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a33776a..c500efcc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [Unpublished Version / DEV] + +### Enhancements & fixes + ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08 ### Credits diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index bafbf577..a8974f98 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/fetchngs + This report has been generated by the nf-core/fetchngs analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-fetchngs-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 3877ed26..912ce43c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -220,7 +220,7 @@ manifest { description = """Pipeline to fetch metadata and raw FastQ files from public databases""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.10.1' + version = '1.11.0dev' doi = 'https://doi.org/10.5281/zenodo.5070524' } From b3d79dfa75875cd518d5bf2d3c93c929737d13d0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 9 Oct 2023 09:59:25 +0200 Subject: [PATCH 107/175] fix conflicts + update initialise + code polish --- .prettierignore | 1 + README.md | 1 + conf/test.config | 2 + main.nf | 13 ++- modules.json | 2 +- nextflow.config | 1 - subworkflows/nf-core/initialise/main.nf | 124 +++++++++++++++++++++-- subworkflows/nf-core/initialise/meta.yml | 34 +++---- 8 files changed, 143 insertions(+), 35 deletions(-) diff --git a/.prettierignore b/.prettierignore index 437d763d..bd464e26 100644 --- a/.prettierignore +++ b/.prettierignore @@ -5,6 +5,7 @@ slackreport.json work/ data/ results/ +.nf-test/ .DS_Store testing/ testing* diff --git a/README.md b/README.md index de90338a..02be6056 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+linting%22) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results) +[![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) diff --git a/conf/test.config b/conf/test.config index 3c58e9cf..cb77f578 100644 --- a/conf/test.config +++ b/conf/test.config @@ -21,4 +21,6 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv' + + validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data' } diff --git a/main.nf b/main.nf index 428273c4..b7445e20 100644 --- a/main.nf +++ b/main.nf @@ -21,10 +21,13 @@ nextflow.enable.dsl = 2 ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } -// Validate input parameters -if (params.validate_params) { - validateParameters() -} +// Read in ids from --input file +Channel + .from(file(params.input, checkIfExists: true)) + .splitCsv(header:false, sep:'', strip:true) + .map { it[0] } + .unique() + .set { ch_ids } // Auto-detect input id type def input_type = '' @@ -85,7 +88,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided // workflow NFCORE_FETCHNGS { - INITIALISE ( params.version, params.help, params.valid_params ) + INITIALISE ( params.version, params.help, params.validate_params, true ) ch_versions = Channel.empty() diff --git a/modules.json b/modules.json index 7bfa0ad2..aebf22de 100644 --- a/modules.json +++ b/modules.json @@ -36,7 +36,7 @@ }, "initialise": { "branch": "master", - "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475", + "git_sha": "8340fb3779fe3233a455aeee1f60ceb203434ab6", "installed_by": ["subworkflows"] } } diff --git a/nextflow.config b/nextflow.config index 8e333cba..8f6f9721 100644 --- a/nextflow.config +++ b/nextflow.config @@ -49,7 +49,6 @@ params { // Schema validation default options validationFailUnrecognisedParams = false validationLenientMode = false - validationSchemaIgnoreParams = 'genomes' validationShowHiddenParams = false validate_params = true diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf index 0cbd3799..31fb1b4c 100644 --- a/subworkflows/nf-core/initialise/main.nf +++ b/subworkflows/nf-core/initialise/main.nf @@ -10,26 +10,34 @@ workflow INITIALISE { version // bool help // bool validate_params // bool + logo // bool main: - // Print workflow version and exit on --version - if (version) { - String version_string = "" + // Get version string for use with --version or printing to log when creating + String version_string = "" + + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } + // Print workflow version and exit on --version + if (version) { log.info "${workflow.manifest.name} ${version_string}" System.exit(0) } + if ( logo ) { + log.info logo(workflow, params.monochrome_logs) + } + log.info "${workflow.manifest.name} ${version_string}" + // Print citation for nf-core def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The nf-core framework\n" + @@ -66,3 +74,97 @@ workflow INITIALISE { summary_params } + +// +// ANSII Colours used for terminal logging +// +def logColours(Boolean monochrome_logs) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// +// Does what is says on the tin +// +def dashedLine(monochrome_logs) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + +// +// nf-core logo +// +def logo(workflow, monochrome_logs) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml index 69596bb5..1d364847 100644 --- a/subworkflows/nf-core/initialise/meta.yml +++ b/subworkflows/nf-core/initialise/meta.yml @@ -6,28 +6,28 @@ keywords: - check - help - version -modules: +components: [] input: - version: - type: boolean - description: | - Structure: val(version) - Boolean to show the pipeline version and exit. + type: boolean + description: | + Structure: val(version) + Boolean to show the pipeline version and exit. - help: - type: boolean - description: | - Structure: val(help) - Boolean to show the pipeline help message and exit. + type: boolean + description: | + Structure: val(help) + Boolean to show the pipeline help message and exit. - validate_params: - type: boolean - description: | - Structure: val(validate_params) - Whether to validate the parameters prior to starting the pipeline. + type: boolean + description: | + Structure: val(validate_params) + Whether to validate the parameters prior to starting the pipeline. output: - summary_params: - type: value - description: | - Structure: val(summary_params) - A map of the parameters used in the pipeline. + type: value + description: | + Structure: val(summary_params) + A map of the parameters used in the pipeline. authors: - "@adamrtalbot" From e37fba215c02025b1a749fe1150edd27eb547c5b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 9 Oct 2023 10:03:32 +0200 Subject: [PATCH 108/175] fix linting --- .nf-core.yml | 3 ++- modules.json | 26 +++++++++++++++++++------- nextflow.config | 1 + 3 files changed, 22 insertions(+), 8 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 78f1faff..8d668011 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,6 +8,7 @@ lint: - conf/modules.config - lib/WorkflowFetchngs.groovy files_unchanged: + - .gitattributes + - .prettierignore - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy - - .gitattributes diff --git a/modules.json b/modules.json index aebf22de..9f6805c1 100644 --- a/modules.json +++ b/modules.json @@ -8,22 +8,30 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/sratoolsncbisettings": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + "installed_by": [ + "fastq_download_prefetch_fasterqdump_sratools" + ] }, "sratools/fasterqdump": { "branch": "master", "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc", - "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + "installed_by": [ + "fastq_download_prefetch_fasterqdump_sratools" + ] }, "sratools/prefetch": { "branch": "master", "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc", - "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + "installed_by": [ + "fastq_download_prefetch_fasterqdump_sratools" + ] } } }, @@ -32,15 +40,19 @@ "fastq_download_prefetch_fasterqdump_sratools": { "branch": "master", "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "initialise": { "branch": "master", "git_sha": "8340fb3779fe3233a455aeee1f60ceb203434ab6", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 8f6f9721..5ad350c9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -50,6 +50,7 @@ params { validationFailUnrecognisedParams = false validationLenientMode = false validationShowHiddenParams = false + validationSchemaIgnoreParams = '' validate_params = true } From e6b7c71767a7f06fa37c8a1ec28d346d15667af6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 9 Oct 2023 10:08:31 +0200 Subject: [PATCH 109/175] prettier --- modules.json | 26 +++++++------------------- 1 file changed, 7 insertions(+), 19 deletions(-) diff --git a/modules.json b/modules.json index 9f6805c1..aebf22de 100644 --- a/modules.json +++ b/modules.json @@ -8,30 +8,22 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/fasterqdump": { "branch": "master", "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc", - "installed_by": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/prefetch": { "branch": "master", "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc", - "installed_by": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] } } }, @@ -40,19 +32,15 @@ "fastq_download_prefetch_fasterqdump_sratools": { "branch": "master", "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "initialise": { "branch": "master", "git_sha": "8340fb3779fe3233a455aeee1f60ceb203434ab6", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From b37087e7da4814eeca851826a62fe8d84724e81c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 9 Oct 2023 11:40:58 +0200 Subject: [PATCH 110/175] use /tmp for nf-test tests --- .gitignore | 15 ++++++++------- nf-test.config | 2 +- workflows/sra/tests/main.nf.test.snap | 2 +- 3 files changed, 10 insertions(+), 9 deletions(-) diff --git a/.gitignore b/.gitignore index b1b5890a..267dd7d9 100644 --- a/.gitignore +++ b/.gitignore @@ -1,11 +1,12 @@ +*.pyc +.DS_Store .nextflow* -work/ +.nf-test.log +.nf-test/ data/ +nf-test results/ -.DS_Store -testing/ +test.xml testing* -*.pyc -.nf-test/ -nf-test -.nf-test.log +testing/ +work/ diff --git a/nf-test.config b/nf-test.config index 0799cb40..cb656b94 100644 --- a/nf-test.config +++ b/nf-test.config @@ -3,7 +3,7 @@ config { testsDir "." // nf-test directory including temporary files for each test - workDir ".nf-test" + workDir "/tmp" // location of library folder that is added automatically to the classpath libDir "lib/" diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 955dd72a..d53f3de2 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-06T12:18:32.149462" + "timestamp": "2023-10-09T11:10:06.701286" } } \ No newline at end of file From cb6d4f34586d7ff0d54dfa3803cd2eebdb161175 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 9 Oct 2023 12:37:44 +0200 Subject: [PATCH 111/175] update snapshots --- .../sra/tests/sra_force_sratools_download.nf.test.snap | 6 +++--- .../sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap | 2 +- .../sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 5cb1876c..a22fad41 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -6,7 +6,7 @@ ], "1": [ - "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" + "samplesheet.csv:md5,f582a7cf6b4a507e3ccbd2ebd134bd26" ], "2": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" @@ -37,7 +37,7 @@ ] ], "samplesheet": [ - "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" + "samplesheet.csv:md5,f582a7cf6b4a507e3ccbd2ebd134bd26" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2023-10-06T12:24:57.695874" + "timestamp": "2023-10-09T12:31:35.173406" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 60cd3444..3e26ff24 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-06T12:03:19.401141" + "timestamp": "2023-10-09T11:48:46.177797" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index c3e9ae8b..cacb42cc 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-06T11:59:31.7356" + "timestamp": "2023-10-09T11:44:49.759545" } } \ No newline at end of file From 07b253567bb9701735fb12469f00fcf19c3d9818 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 10 Oct 2023 10:57:10 +0100 Subject: [PATCH 112/175] Remove nf-test files from .gitattributes --- .gitattributes | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitattributes b/.gitattributes index c1c17000..7a2dabc2 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,5 +1,4 @@ *.config linguist-language=nextflow *.nf.test linguist-language=nextflow -tests/**/*nf.test.snap linguist-generated modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated From 7169d6bf31a6ca86cd0ccfb6093549867873ab42 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 10 Oct 2023 10:57:31 +0100 Subject: [PATCH 113/175] Remove unused multiqc_config.yml --- assets/multiqc_config.yml | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 assets/multiqc_config.yml diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml deleted file mode 100644 index a8974f98..00000000 --- a/assets/multiqc_config.yml +++ /dev/null @@ -1,13 +0,0 @@ -report_comment: > - This report has been generated by the nf-core/fetchngs - analysis pipeline. For information about how to interpret these results, please see the - documentation. -report_section_order: - "nf-core-fetchngs-methods-description": - order: -1000 - software_versions: - order: -1001 - "nf-core-fetchngs-summary": - order: -1002 - -export_plots: true From 728360ce4c69f956ea11cc8cc6dd2b8456558d3e Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 10 Oct 2023 12:39:36 +0200 Subject: [PATCH 114/175] Update main.nf --- main.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/main.nf b/main.nf index b7445e20..d6c239a0 100644 --- a/main.nf +++ b/main.nf @@ -17,6 +17,8 @@ nextflow.enable.dsl = 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation' + // Check if --input file is empty ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } From 4d9a38dcdc42fbbe341ff6860ff57bbbff4ef564 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 10 Oct 2023 12:42:22 +0200 Subject: [PATCH 115/175] Apply suggestions from code review --- .gitignore | 1 - .nf-core.yml | 1 - .prettierignore | 1 - 3 files changed, 3 deletions(-) diff --git a/.gitignore b/.gitignore index 267dd7d9..ff233cdb 100644 --- a/.gitignore +++ b/.gitignore @@ -2,7 +2,6 @@ .DS_Store .nextflow* .nf-test.log -.nf-test/ data/ nf-test results/ diff --git a/.nf-core.yml b/.nf-core.yml index 8d668011..143f4821 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,6 +9,5 @@ lint: - lib/WorkflowFetchngs.groovy files_unchanged: - .gitattributes - - .prettierignore - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy diff --git a/.prettierignore b/.prettierignore index bd464e26..437d763d 100644 --- a/.prettierignore +++ b/.prettierignore @@ -5,7 +5,6 @@ slackreport.json work/ data/ results/ -.nf-test/ .DS_Store testing/ testing* From 56abd32f7a81e812b449b79bd1abf960448387fa Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 10 Oct 2023 14:22:14 +0200 Subject: [PATCH 116/175] Apply suggestions from code review --- .nf-core.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.nf-core.yml b/.nf-core.yml index 143f4821..bb27a4e9 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -9,5 +9,6 @@ lint: - lib/WorkflowFetchngs.groovy files_unchanged: - .gitattributes + - .gitignore - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy From 538cc2339fd7be0748cf93f2b5693054faf8c593 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 10 Oct 2023 14:47:47 +0100 Subject: [PATCH 117/175] Per module/subworkflow tags.yml file Changes: - Add separate tags.yml files for all modules and subworkflows that featured in the original tags.yml file. - Removes old tags.yml file - Adds github action to combine all tags.yml files for pattern matching using yq --- .github/workflows/ci.yml | 9 ++++++++- .../local/multiqc_mappings_config/tests/tags.yml | 2 ++ modules/local/sra_fastq_ftp/tests/tags.yml | 2 ++ modules/local/sra_ids_to_runinfo/tests/tags.yml | 2 ++ .../local/sra_merge_samplesheet/tests/tags.yml | 2 ++ modules/local/sra_runinfo_to_ftp/tests/tags.yml | 2 ++ modules/local/sra_to_samplesheet/tests/tags.yml | 2 ++ {.github => workflows/sra/tests}/tags.yml | 15 --------------- 8 files changed, 20 insertions(+), 16 deletions(-) create mode 100644 modules/local/multiqc_mappings_config/tests/tags.yml create mode 100644 modules/local/sra_fastq_ftp/tests/tags.yml create mode 100644 modules/local/sra_ids_to_runinfo/tests/tags.yml create mode 100644 modules/local/sra_merge_samplesheet/tests/tags.yml create mode 100644 modules/local/sra_runinfo_to_ftp/tests/tags.yml create mode 100644 modules/local/sra_to_samplesheet/tests/tags.yml rename {.github => workflows/sra/tests}/tags.yml (83%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 68e2773c..9273f90e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -30,10 +30,17 @@ jobs: tags: ${{ steps.filter.outputs.changes }} steps: - uses: actions/checkout@v3 + - name: Combine all tags.yml files + id: get_username + uses: mikefarah/yq@master + with: + cmd: find . -name "tags.yml" -type f -exec yq ea '. as $item ireduce ({}; . * $item )' {} + > tags.yml + - name: debug + run: cat tags.yml - uses: dorny/paths-filter@v2 id: filter with: - filters: ".github/tags.yml" + filters: "tags.yml" define_nxf_versions: name: Choose nextflow versions to test against depending on target branch diff --git a/modules/local/multiqc_mappings_config/tests/tags.yml b/modules/local/multiqc_mappings_config/tests/tags.yml new file mode 100644 index 00000000..595e2e31 --- /dev/null +++ b/modules/local/multiqc_mappings_config/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc_mappings_config: + - modules/local/multiqc_mappings_config/** diff --git a/modules/local/sra_fastq_ftp/tests/tags.yml b/modules/local/sra_fastq_ftp/tests/tags.yml new file mode 100644 index 00000000..e7474bef --- /dev/null +++ b/modules/local/sra_fastq_ftp/tests/tags.yml @@ -0,0 +1,2 @@ +sra_fastq_ftp: + - modules/local/sra_fastq_ftp/** diff --git a/modules/local/sra_ids_to_runinfo/tests/tags.yml b/modules/local/sra_ids_to_runinfo/tests/tags.yml new file mode 100644 index 00000000..63ea7db3 --- /dev/null +++ b/modules/local/sra_ids_to_runinfo/tests/tags.yml @@ -0,0 +1,2 @@ +sra_ids_to_runinfo: + - modules/local/sra_ids_to_runinfo/** diff --git a/modules/local/sra_merge_samplesheet/tests/tags.yml b/modules/local/sra_merge_samplesheet/tests/tags.yml new file mode 100644 index 00000000..a4292b70 --- /dev/null +++ b/modules/local/sra_merge_samplesheet/tests/tags.yml @@ -0,0 +1,2 @@ +sra_merge_samplesheet: + - modules/local/sra_merge_samplesheet/** diff --git a/modules/local/sra_runinfo_to_ftp/tests/tags.yml b/modules/local/sra_runinfo_to_ftp/tests/tags.yml new file mode 100644 index 00000000..0987a1e6 --- /dev/null +++ b/modules/local/sra_runinfo_to_ftp/tests/tags.yml @@ -0,0 +1,2 @@ +sra_runinfo_to_ftp: + - modules/local/sra_runinfo_to_ftp/** diff --git a/modules/local/sra_to_samplesheet/tests/tags.yml b/modules/local/sra_to_samplesheet/tests/tags.yml new file mode 100644 index 00000000..2f2d527b --- /dev/null +++ b/modules/local/sra_to_samplesheet/tests/tags.yml @@ -0,0 +1,2 @@ +sra_to_samplesheet: + - modules/local/sra_to_samplesheet/** diff --git a/.github/tags.yml b/workflows/sra/tests/tags.yml similarity index 83% rename from .github/tags.yml rename to workflows/sra/tests/tags.yml index 03569f78..52c3e591 100644 --- a/.github/tags.yml +++ b/workflows/sra/tests/tags.yml @@ -1,18 +1,3 @@ -# local modules -multiqc_mappings_config: - - modules/local/multiqc_mappings_config/** -sra_fastq_ftp: - - modules/local/sra_fastq_ftp/** -sra_ids_to_runinfo: - - modules/local/sra_ids_to_runinfo/** -sra_merge_samplesheet: - - modules/local/sra_merge_samplesheet/** -sra_runinfo_to_ftp: - - modules/local/sra_runinfo_to_ftp/** -sra_to_samplesheet: - - modules/local/sra_to_samplesheet/** - -# workflow: sra sra_custom_ena_metadata_fields: - modules/local/sra_ids_to_runinfo/** - modules/local/sra_runinfo_to_ftp/** From ff7fa147b662aed6949b278271784a8da8478a4b Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 10 Oct 2023 14:55:34 +0100 Subject: [PATCH 118/175] Escape single quotes --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9273f90e..63dede75 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: id: get_username uses: mikefarah/yq@master with: - cmd: find . -name "tags.yml" -type f -exec yq ea '. as $item ireduce ({}; . * $item )' {} + > tags.yml + cmd: find . -name "tags.yml" -type f -exec yq ea \'. as $item ireduce ({}; . * $item )\' {} + > tags.yml - name: debug run: cat tags.yml - uses: dorny/paths-filter@v2 From d15e6bec17185b5d9591b8bcab4641fad50df5a7 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 10 Oct 2023 15:02:54 +0100 Subject: [PATCH 119/175] quote command line --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 63dede75..13b86c93 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: id: get_username uses: mikefarah/yq@master with: - cmd: find . -name "tags.yml" -type f -exec yq ea \'. as $item ireduce ({}; . * $item )\' {} + > tags.yml + cmd: "find . -name 'tags.yml' -type f -exec yq ea '. as $item ireduce ({}; . * $item )' {} + > tags.yml" - name: debug run: cat tags.yml - uses: dorny/paths-filter@v2 From 264be7a9abe09c6d4862dec05b3126941f2831a6 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 10 Oct 2023 15:06:33 +0100 Subject: [PATCH 120/175] escape AND quote --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 13b86c93..c1ba3574 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: id: get_username uses: mikefarah/yq@master with: - cmd: "find . -name 'tags.yml' -type f -exec yq ea '. as $item ireduce ({}; . * $item )' {} + > tags.yml" + cmd: "find . -name 'tags.yml' -type f -exec yq ea '. as $item ireduce (\\{\\}; . * $item )' {} + > tags.yml" - name: debug run: cat tags.yml - uses: dorny/paths-filter@v2 From 4f1e6388983c4674a7b3d28cf4b85fec35e4ac75 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 10 Oct 2023 15:20:37 +0100 Subject: [PATCH 121/175] Trying to use cat --- .github/workflows/ci.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c1ba3574..85e53716 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,15 +32,13 @@ jobs: - uses: actions/checkout@v3 - name: Combine all tags.yml files id: get_username - uses: mikefarah/yq@master - with: - cmd: "find . -name 'tags.yml' -type f -exec yq ea '. as $item ireduce (\\{\\}; . * $item )' {} + > tags.yml" + run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml - name: debug run: cat tags.yml - uses: dorny/paths-filter@v2 id: filter with: - filters: "tags.yml" + filters: ".github/tags.yml" define_nxf_versions: name: Choose nextflow versions to test against depending on target branch From 051588c227232ae0a59872eece21b1e4b2e96d3a Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 10 Oct 2023 15:21:35 +0100 Subject: [PATCH 122/175] fixup --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 85e53716..436b61a5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: id: get_username run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml - name: debug - run: cat tags.yml + run: cat .github/tags.yml - uses: dorny/paths-filter@v2 id: filter with: From f81daf8e922b14ee500619d16da37ad98defe572 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 11 Oct 2023 12:02:14 +0100 Subject: [PATCH 123/175] Remove all files in lib directory --- lib/NfcoreTemplate.groovy | 330 ------------------------------ lib/Utils.groovy | 47 ----- lib/WorkflowMain.groovy | 216 ------------------- lib/nfcore_external_java_deps.jar | Bin 2291171 -> 0 bytes 4 files changed, 593 deletions(-) delete mode 100755 lib/NfcoreTemplate.groovy delete mode 100644 lib/Utils.groovy delete mode 100755 lib/WorkflowMain.groovy delete mode 100644 lib/nfcore_external_java_deps.jar diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy deleted file mode 100755 index ed58a7ae..00000000 --- a/lib/NfcoreTemplate.groovy +++ /dev/null @@ -1,330 +0,0 @@ -// -// This file holds several functions used within the nf-core pipeline template. -// - -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput - -class NfcoreTemplate { - - // - // Check AWS Batch related parameters have been specified correctly - // - public static void awsBatch(workflow, params) { - if (workflow.profile.contains('awsbatch')) { - // Check params.awsqueue and params.awsregion have been set if running on AWSBatch - assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - } - } - - // - // Warn if a -profile or Nextflow config has not been provided to run the pipeline - // - public static void checkConfigProvided(workflow, log) { - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - } - - // - // Generate version string - // - public static String version(workflow) { - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string - } - - // - // Construct and send completion email - // - public static void email(workflow, params, summary_params, projectDir, log) { - - // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" - } - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = NfcoreTemplate.version(workflow) - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // Check if we are only sending emails on failure - def email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$projectDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$projectDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir" ] - def sf = new File("$projectDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - Map colors = logColours(params.monochrome_logs) - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" - } - } - - // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - } - - // - // Construct and send a notification to a web server as JSON - // e.g. Microsoft Teams and Slack - // - public static void IM_notification(workflow, params, summary_params, projectDir, log) { - def hook_url = params.hook_url - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = NfcoreTemplate.version(workflow) - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("$projectDir/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); - } - } - - // - // Dump pipeline parameters in a json file - // - public static void dump_parameters(workflow, params) { - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def output_pf = new File(output_d, "params_${timestamp}.json") - def jsonStr = JsonOutput.toJson(params) - output_pf.text = JsonOutput.prettyPrint(jsonStr) - } - - // - // Print pipeline summary on completion - // - public static void summary(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" - } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } - } - - // - // ANSII Colours used for terminal logging - // - public static Map logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes - } - - // - // Does what is says on the tin - // - public static String dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" - } - - // - // nf-core logo - // - public static String logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String workflow_version = NfcoreTemplate.version(workflow) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) - } -} diff --git a/lib/Utils.groovy b/lib/Utils.groovy deleted file mode 100644 index 8d030f4e..00000000 --- a/lib/Utils.groovy +++ /dev/null @@ -1,47 +0,0 @@ -// -// This file holds several Groovy functions that could be useful for any Nextflow pipeline -// - -import org.yaml.snakeyaml.Yaml - -class Utils { - - // - // When running with -profile conda, warn if channels have not been set-up appropriately - // - public static void checkCondaChannels(log) { - Yaml parser = new Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } - - if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy deleted file mode 100755 index 4ec4029a..00000000 --- a/lib/WorkflowMain.groovy +++ /dev/null @@ -1,216 +0,0 @@ -// -// This file holds several functions specific to the main.nf workflow in the nf-core/fetchngs pipeline -// - -import nextflow.Nextflow - -class WorkflowMain { - - // - // Citation string for pipeline - // - public static String citation(workflow) { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - " https://doi.org/10.5281/zenodo.5070524\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" - } - - - // - // Validate parameters and print summary to screen - // - public static void initialise(workflow, params, log) { - - // Print workflow version and exit on --version - if (params.version) { - String workflow_version = NfcoreTemplate.version(workflow) - log.info "${workflow.manifest.name} ${workflow_version}" - System.exit(0) - } - - // Check that a -profile or Nextflow config has been provided to run the pipeline - NfcoreTemplate.checkConfigProvided(workflow, log) - - // Check that conda channels are set-up correctly - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - Utils.checkCondaChannels(log) - } - - // Check AWS batch settings - NfcoreTemplate.awsBatch(workflow, params) - - // Check input has been provided - if (!params.input) { - Nextflow.error("Please provide an input file containing ids to the pipeline - one per line e.g. '--input ids.csv'") - } - - // Check valid input_type has been provided - def input_types = ['sra', 'synapse'] - if (!input_types.contains(params.input_type)) { - Nextflow.error("Invalid option: '${params.input_type}'. Valid options for '--input_type': ${input_types.join(', ')}.") - } - } - - // Check if input ids are from the SRA - public static Boolean isSraId(input) { - def is_sra = false - def total_ids = 0 - def no_match_ids = [] - def pattern = /^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM]))(\d+)$/ - input.eachLine { line -> - total_ids += 1 - if (!(line =~ pattern)) { - no_match_ids << line - } - } - - def num_match = total_ids - no_match_ids.size() - if (num_match > 0) { - if (num_match == total_ids) { - is_sra = true - } else { - Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!") - } - } - return is_sra - } - - // Check if input ids are from the Synapse platform - public static Boolean isSynapseId(input) { - def is_synapse = false - def total_ids = 0 - def no_match_ids = [] - def pattern = /^syn\d{8}$/ - input.eachLine { line -> - total_ids += 1 - if (!(line =~ pattern)) { - no_match_ids << line - } - } - - def num_match = total_ids - no_match_ids.size() - if (num_match > 0) { - if (num_match == total_ids) { - is_synapse = true - } else { - Nextflow.error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!") - } - } - return is_synapse - } - - // - // Check and validate parameters - // - public static void sraInitialise(params, valid_params) { - // Check minimal ENA fields are provided to download FastQ files - def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields'] - if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) { - Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'") - } - } - - // - // Print a warning after pipeline has completed - // - public static void sraCurateSamplesheetWarn(log) { - log.warn "=============================================================================\n" + - " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + - " Public databases don't reliably hold information such as strandedness\n" + - " information, controls etc\n\n" + - " All of the sample metadata obtained from the ENA has been appended\n" + - " as additional columns to help you manually curate the samplesheet before\n" + - " running nf-core/other pipelines.\n" + - "===================================================================================" - } - - // - // Convert metadata obtained from the 'synapse show' command to a Groovy map - // - public static Map synapseShowToMap(synapse_file) { - def meta = [:] - def category = '' - synapse_file.eachLine { line -> - def entries = [null, null] - if (!line.startsWith(' ') && !line.trim().isEmpty()) { - category = line.tokenize(':')[0] - } else { - entries = line.trim().tokenize('=') - } - meta["${category}|${entries[0]}"] = entries[1] - } - meta.id = meta['properties|id'] - meta.name = meta['properties|name'] - meta.md5 = meta['File|md5'] - return meta.findAll{ it.value != null } - } - - // - // Print a warning after pipeline has completed - // - public static void synapseCurateSamplesheetWarn(log) { - log.warn "=============================================================================\n" + - " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + - " Where applicable, default values will be used for sample-specific metadata\n" + - " such as strandedness, controls etc as this information is not provided\n" + - " in a standardised manner when uploading data to Synapse.\n" + - 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zR(SliZInVGdFiX-+?ulq^Pr062u)ng5j(}CTiGLQkv6?rkcPd!;?fH5U^+iRKzvfu zV~;6qm0a{ko%Q&bhwCxwcNjHtrRuX~uPJ4SI{~}WvHI=pn{11L;PnA=|26zUHCTRb zgzHKw^0*vqpCo`j;lJKoyKx8d7!8AI%m}wVX-c@2B_KnHw}>4U#aDXTOq7<|Wd4Tsc3c@~MlU!Do- z;44!I44#TL{egGhbo--w?_)Cnawj*O*6B(*W)rTAlB^EKDv_8PPE_4zdul@}vk=<2 zWM<}+1wca(EgDR~^?BHoZ|m^g5Plb!5RP%HK2`I`LZtE_&_TmfZv$SS=39Ykn@g)h zK2xOBBV8(O>$B1^yv5v)z{*v8xsq2EHw6IY)|ObEUM$)D;2ldBzXL^o2#D*TR7q2+ zDkW3pWRJ7P86=mB!#~|iPx<77n)$##FJ%f5Y(taKVql$zJJ-sa2Lq?0v^>t=^){tS z15cnLfeqNGIDqY|K4E1|Nz)c>_jNb-`iKXYX>tUy3D1%=D4xIVLh5@N-8J$JWP1}C zk1ce0UGgFBPREZ`^YsLWgRZcTtn1;*uP{d&`VCLk^-43Sr>Q}8Ke)}JYvPzo( From 7a46eb97226099e062c71e1daf74fbeb6270dc29 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 11 Oct 2023 12:02:39 +0100 Subject: [PATCH 124/175] Remove nf-core/initialise subworkflow --- modules.json | 5 - subworkflows/nf-core/initialise/main.nf | 170 ----------------------- subworkflows/nf-core/initialise/meta.yml | 33 ----- 3 files changed, 208 deletions(-) delete mode 100644 subworkflows/nf-core/initialise/main.nf delete mode 100644 subworkflows/nf-core/initialise/meta.yml diff --git a/modules.json b/modules.json index aebf22de..6dd402db 100644 --- a/modules.json +++ b/modules.json @@ -33,11 +33,6 @@ "branch": "master", "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", "installed_by": ["subworkflows"] - }, - "initialise": { - "branch": "master", - "git_sha": "8340fb3779fe3233a455aeee1f60ceb203434ab6", - "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf deleted file mode 100644 index 31fb1b4c..00000000 --- a/subworkflows/nf-core/initialise/main.nf +++ /dev/null @@ -1,170 +0,0 @@ -// This is a reimplementation of the basic initialise methods in the nf-core template -// The role of this subworkflow is to check the input parameters and print help messages -// Use this to start your nf-core pipeline - -include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation' - -workflow INITIALISE { - - take: - version // bool - help // bool - validate_params // bool - logo // bool - - main: - - // Get version string for use with --version or printing to log when creating - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - // Print workflow version and exit on --version - if (version) { - log.info "${workflow.manifest.name} ${version_string}" - System.exit(0) - } - - if ( logo ) { - log.info logo(workflow, params.monochrome_logs) - } - log.info "${workflow.manifest.name} ${version_string}" - - // Print citation for nf-core - def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " ${workflow.manifest.homePage}/blob/master/CITATIONS.md" - log.info citation - - // Print help message if needed - if (params.help) { - def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker" - log.info paramsHelp(command) - System.exit(0) - } - - if ( params.validate_params != false ){ - validateParameters() - } - - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - - log.info paramsSummaryLog(workflow) - - summary_params = paramsSummaryMap(workflow) - - emit: - summary_params - -} - -// -// ANSII Colours used for terminal logging -// -def logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes -} - -// -// Does what is says on the tin -// -def dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - -// -// nf-core logo -// -def logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml deleted file mode 100644 index 1d364847..00000000 --- a/subworkflows/nf-core/initialise/meta.yml +++ /dev/null @@ -1,33 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "initialise" -description: Validate input parameters and print help messages -keywords: - - admin - - check - - help - - version -components: [] -input: - - version: - type: boolean - description: | - Structure: val(version) - Boolean to show the pipeline version and exit. - - help: - type: boolean - description: | - Structure: val(help) - Boolean to show the pipeline help message and exit. - - validate_params: - type: boolean - description: | - Structure: val(validate_params) - Whether to validate the parameters prior to starting the pipeline. -output: - - summary_params: - type: value - description: | - Structure: val(summary_params) - A map of the parameters used in the pipeline. -authors: - - "@adamrtalbot" From d88b631acbb86271e66077517a639bea99b432da Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 11 Oct 2023 12:10:36 +0100 Subject: [PATCH 125/175] Update workflow main scripts --- main.nf | 111 ++++++++++++++------------------------ workflows/sra/main.nf | 24 ++++----- workflows/synapse/main.nf | 6 +-- 3 files changed, 53 insertions(+), 88 deletions(-) diff --git a/main.nf b/main.nf index b7445e20..7794d1b9 100644 --- a/main.nf +++ b/main.nf @@ -13,99 +13,42 @@ nextflow.enable.dsl = 2 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE & PRINT PARAMETER SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// Check if --input file is empty -ch_input = file(params.input, checkIfExists: true) -if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } - -// Read in ids from --input file -Channel - .from(file(params.input, checkIfExists: true)) - .splitCsv(header:false, sep:'', strip:true) - .map { it[0] } - .unique() - .set { ch_ids } - -// Auto-detect input id type -def input_type = '' -if (WorkflowMain.isSraId(ch_input)) { - input_type = 'sra' -} else if (WorkflowMain.isSynapseId(ch_input)) { - input_type = 'synapse' -} else { - error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') -} - -if (params.input_type != input_type) { - error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") -} - -if (params.input_type == 'sra') { - def valid_params = [ - ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5'] - ] - - // Validate input parameters - WorkflowMain.sraInitialise(params, valid_params) -} else if (params.input_type == 'synapse') { - - // Create channel for synapse config - if (params.synapse_config) { - ch_synapse_config = file(params.synapse_config, checkIfExists: true) - } else { - error('Please provide a Synapse config file for download authentication!') - } -} - -/* -======================================================================================== - IMPORT MODULES/SUBWORKFLOWS -======================================================================================== -*/ - -include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' -include { INITIALISE } from './subworkflows/nf-core/initialise/main' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT WORKFLOWS + NAMED WORKFLOWS FOR PIPELINE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ if (params.input_type == 'sra') include { SRA } from './workflows/sra' if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse' -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOWS FOR PIPELINE -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - // // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided // workflow NFCORE_FETCHNGS { - INITIALISE ( params.version, params.help, params.validate_params, true ) + take: + ids // channel: database ids read in from --input + + main: + ch_versions = Channel.empty() // // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids // if (params.input_type == 'sra') { - SRA ( ch_ids ) - ch_versions = ch_versions.mix(SRA.out.versions) + SRA ( ids ) + ch_versions = SRA.out.versions // // WORKFLOW: Download FastQ files for Synapse ids // } else if (params.input_type == 'synapse') { - SYNAPSE ( ch_ids, ch_synapse_config ) - ch_versions = ch_versions.mix(SYNAPSE.out.versions) + SYNAPSE ( ids ) + ch_versions = SYNAPSE.out.versions } + + emit: + versions = ch_versions } /* @@ -114,12 +57,36 @@ workflow NFCORE_FETCHNGS { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { PIPELINE_INITIALISATION } from './subworkflows/local/nf_core_fetchngs_utils' +include { PIPELINE_COMPLETION } from './subworkflows/local/nf_core_fetchngs_utils' + // // WORKFLOW: Execute a single named workflow for the pipeline -// See: https://github.com/nf-core/rnaseq/issues/619 // workflow { - NFCORE_FETCHNGS () + + // + // SUBWORKFLOW: Run initialisation tasks + // + PIPELINE_INITIALISATION () + + // + // WORKFLOW: Run primary workflows for the pipeline + // + NFCORE_FETCHNGS ( + PIPELINE_INITIALISATION.out.ids + ) + + // + // SUBWORKFLOW: Run completion tasks + // + PIPELINE_COMPLETION ( + NFCORE_FETCHNGS.out.versions, + params.input_type, + params.email, + params.email_on_fail, + PIPELINE_INITIALISATION.out.summary_params + ) } /* diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 3fd22f5d..a8f54646 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -62,10 +62,7 @@ workflow SRA { .unique() .set { ch_sra_metadata } - ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first()) - fastq_files = Channel.empty() - if (!params.skip_fastq_download) { ch_sra_metadata @@ -97,18 +94,19 @@ workflow SRA { ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first()) // Isolate FASTQ channel which will be added to emit block - fastq_files.mix( - SRA_FASTQ_FTP.out.fastq, - FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads - ).map { meta, fastq -> - def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] - def meta_clone = meta.clone() + fastq_files + .mix(SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads) + .map { + meta, fastq -> + def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] + def meta_clone = meta.clone() - meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : '' - meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : '' + meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : '' + meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : '' - return meta_clone - }.set { ch_sra_metadata } + return meta_clone + } + .set { ch_sra_metadata } } // diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index d2681866..6b5ea02c 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -106,9 +106,9 @@ workflow SYNAPSE { ch_versions = ch_versions.mix(SYNAPSE_MERGE_SAMPLESHEET.out.versions) emit: - fastq = ch_fastq - samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet - versions = ch_versions.unique() + fastq = ch_fastq + samplesheet = SYNAPSE_MERGE_SAMPLESHEET.out.samplesheet + versions = ch_versions.unique() } /* From 4328622547fb3a1119f412ded0dd8b752981ec35 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 11 Oct 2023 12:10:57 +0100 Subject: [PATCH 126/175] Add subworkflows to replace files in lib directory --- .../local/nextflow_pipeline_utils/main.nf | 123 +++++++ .../local/nf_core_fetchngs_utils/main.nf | 296 +++++++++++++++++ .../local/nf_core_pipeline_utils/main.nf | 308 ++++++++++++++++++ .../local/nf_validation_plugin_utils/main.nf | 52 +++ 4 files changed, 779 insertions(+) create mode 100644 subworkflows/local/nextflow_pipeline_utils/main.nf create mode 100644 subworkflows/local/nf_core_fetchngs_utils/main.nf create mode 100644 subworkflows/local/nf_core_pipeline_utils/main.nf create mode 100644 subworkflows/local/nf_validation_plugin_utils/main.nf diff --git a/subworkflows/local/nextflow_pipeline_utils/main.nf b/subworkflows/local/nextflow_pipeline_utils/main.nf new file mode 100644 index 00000000..e56394ed --- /dev/null +++ b/subworkflows/local/nextflow_pipeline_utils/main.nf @@ -0,0 +1,123 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow NEXTFLOW_PIPELINE_UTILS { + + take: + print_version // bool + dump_parameters // bool + output_directory // path: base directory used to publish pipeline results + check_conda_channels // bool + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && output_directory) { + dumpParametersToJSON(output_directory) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(output_directory) { + def output_d = new File("${output_directory}/pipeline_info/") + if (!output_d.exists()) { + output_d.mkdirs() + } + + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def output_pf = new File(output_d, "params_${timestamp}.json") + def jsonStr = JsonOutput.toJson(params) + output_pf.text = JsonOutput.prettyPrint(jsonStr) +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + Yaml parser = new Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } + + if (channels_missing | channel_priority_violation) { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + } +} diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf new file mode 100644 index 00000000..129b2e3f --- /dev/null +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -0,0 +1,296 @@ +// +// Subworkflow with functionality specific to the nf-core/fetchngs pipeline +// + +/* +======================================================================================== + IMPORT MODULES/SUBWORKFLOWS +======================================================================================== +*/ + +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../modules/nf-core/custom/dumpsoftwareversions' +include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../nextflow_pipeline_utils' +include { NF_VALIDATION_PLUGIN_UTILS } from '../nf_validation_plugin_utils' +include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary } from '../nf_core_pipeline_utils' + +/* +======================================================================================== + SUBWORKFLOW TO INITIALISE PIPELINE +======================================================================================== +*/ + +workflow PIPELINE_INITIALISATION { + + main: + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + NEXTFLOW_PIPELINE_UTILS ( + params.version, + true, + params.outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + def pre_help_text = nfCoreLogo(getWorkflowVersion()) + def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine() + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input ids.csv --outdir " + NF_VALIDATION_PLUGIN_UTILS ( + params.help, + workflow_command, + pre_help_text, + post_help_text, + params.validate_params + ) + + // + // Check config provided to the pipeline + // + NF_CORE_PIPELINE_UTILS () + + // + // Auto-detect input id type + // + ch_input = file(params.input) + def input_type = '' + if (isSraId(ch_input)) { + input_type = 'sra' + sraCheckENAMetadataFields() + } else if (isSynapseId(ch_input)) { + input_type = 'synapse' + } else { + error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') + } + + if (params.input_type != input_type) { + error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") + } + + // Read in ids from --input file + Channel + .from(ch_input) + .splitCsv(header:false, sep:'', strip:true) + .map { it[0] } + .unique() + .set { ch_ids } + + emit: + ids = ch_ids + summary_params = NF_VALIDATION_PLUGIN_UTILS.out.summary_params +} + +/* +======================================================================================== + SUBWORKFLOW FOR PIPELINE COMPLETION +======================================================================================== +*/ + +workflow PIPELINE_COMPLETION { + + take: + versions // channel: software tools versions + input_type // string: 'sra' or 'synapse' + email // string: email address + email_on_fail // string: email address sent on pipeline failure + summary_params // map: Groovy map of the parameters used in the pipeline + + main: + + // + // MODULE: Dump software versions for all tools used in the workflow + // + CUSTOM_DUMPSOFTWAREVERSIONS ( + versions.collectFile(name: 'collated_versions.yml') + ) + + // + // Completion email and summary + // + workflow.onComplete { + if (email || email_on_fail) { + completionEmail(summary_params) + } + + completionSummary() + + if (input_type == 'sra') { + sraCurateSamplesheetWarn() + } else if (input_type == 'synapse') { + synapseCurateSamplesheetWarn() + } + } +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Check if input ids are from the SRA +// +def isSraId(input) { + def is_sra = false + def total_ids = 0 + def no_match_ids = [] + def pattern = /^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM]))(\d+)$/ + input.eachLine { line -> + total_ids += 1 + if (!(line =~ pattern)) { + no_match_ids << line + } + } + + def num_match = total_ids - no_match_ids.size() + if (num_match > 0) { + if (num_match == total_ids) { + is_sra = true + } else { + error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!") + } + } + return is_sra +} + +// +// Check if input ids are from the Synapse platform +// +def isSynapseId(input) { + def is_synapse = false + def total_ids = 0 + def no_match_ids = [] + def pattern = /^syn\d{8}$/ + input.eachLine { line -> + total_ids += 1 + if (!(line =~ pattern)) { + no_match_ids << line + } + } + + def num_match = total_ids - no_match_ids.size() + if (num_match > 0) { + if (num_match == total_ids) { + is_synapse = true + } else { + error("Mixture of ids provided via --input: ${no_match_ids.join(', ')}\nPlease provide either SRA / ENA / GEO / DDBJ or Synapse ids!") + } + } + return is_synapse +} + +// +// Check and validate parameters +// +def sraCheckENAMetadataFields() { + // Check minimal ENA fields are provided to download FastQ files + def valid_ena_metadata_fields = ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5'] + def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_ena_metadata_fields + if (!ena_metadata_fields.containsAll(valid_ena_metadata_fields)) { + error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_ena_metadata_fields.join(',')}'") + } +} + +// +// Print a warning after pipeline has completed +// +def sraCurateSamplesheetWarn() { + log.warn "=============================================================================\n" + + " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + + " Public databases don't reliably hold information such as strandedness\n" + + " information, controls etc\n\n" + + " All of the sample metadata obtained from the ENA has been appended\n" + + " as additional columns to help you manually curate the samplesheet before\n" + + " running nf-core/other pipelines.\n" + + "===================================================================================" +} + +// +// Convert metadata obtained from the 'synapse show' command to a Groovy map +// +def synapseShowToMap(synapse_file) { + def meta = [:] + def category = '' + synapse_file.eachLine { line -> + def entries = [null, null] + if (!line.startsWith(' ') && !line.trim().isEmpty()) { + category = line.tokenize(':')[0] + } else { + entries = line.trim().tokenize('=') + } + meta["${category}|${entries[0]}"] = entries[1] + } + meta.id = meta['properties|id'] + meta.name = meta['properties|name'] + meta.md5 = meta['File|md5'] + return meta.findAll{ it.value != null } +} + +// +// Print a warning after pipeline has completed +// +def synapseCurateSamplesheetWarn() { + log.warn "=============================================================================\n" + + " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + + " Where applicable, default values will be used for sample-specific metadata\n" + + " such as strandedness, controls etc as this information is not provided\n" + + " in a standardised manner when uploading data to Synapse.\n" + + "===================================================================================" +} + +// +// Obtain Sample ID from File Name +// +def synapseSampleNameFromFastQ(input_file, pattern) { + + def sampleids = "" + + def filePattern = pattern.toString() + int p = filePattern.lastIndexOf('/') + if( p != -1 ) + filePattern = filePattern.substring(p+1) + + input_file.each { + String fileName = input_file.getFileName().toString() + + String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' } + String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' } + if( indexOfWildcards==-1 && indexOfBrackets==-1 ) { + if( fileName == filePattern ) + return actual.getSimpleName() + throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName") + } + + int groupCount = 0 + for( int i=0; i w << email_html } + def output_tf = new File(output_d, "pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } +} + +// +// Print pipeline summary on completion +// +def completionSummary() { + Map colors = logColours() + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params) { + def hook_url = params.hook_url + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = NfcoreTemplate.version(workflow) + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } +} diff --git a/subworkflows/local/nf_validation_plugin_utils/main.nf b/subworkflows/local/nf_validation_plugin_utils/main.nf new file mode 100644 index 00000000..be815a7f --- /dev/null +++ b/subworkflows/local/nf_validation_plugin_utils/main.nf @@ -0,0 +1,52 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow NF_VALIDATION_PLUGIN_UTILS { + + take: + print_help // bool + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // bool + + main: + + // + // Print help message if needed + // + if (print_help && workflow_command) { + log.info pre_help_text + paramsHelp(workflow_command) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters() + } + + emit: + summary_params = paramsSummaryMap(workflow) +} From 2f68d1efa8bfb77b3d2a3088526e4971fb96a346 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 11 Oct 2023 12:26:26 +0100 Subject: [PATCH 127/175] Invoke imNotification in completion subworkflow --- main.nf | 1 + subworkflows/local/nf_core_fetchngs_utils/main.nf | 7 ++++++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 7794d1b9..6d3ea228 100644 --- a/main.nf +++ b/main.nf @@ -85,6 +85,7 @@ workflow { params.input_type, params.email, params.email_on_fail, + params.hook_url, PIPELINE_INITIALISATION.out.summary_params ) } diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index 129b2e3f..5cc2162b 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -11,7 +11,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../modules/nf-core/custom/dumpsoftwareversions' include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../nextflow_pipeline_utils' include { NF_VALIDATION_PLUGIN_UTILS } from '../nf_validation_plugin_utils' -include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary } from '../nf_core_pipeline_utils' +include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils' /* ======================================================================================== @@ -96,6 +96,7 @@ workflow PIPELINE_COMPLETION { input_type // string: 'sra' or 'synapse' email // string: email address email_on_fail // string: email address sent on pipeline failure + hook_url // string: hook URL for notifications summary_params // map: Groovy map of the parameters used in the pipeline main: @@ -117,6 +118,10 @@ workflow PIPELINE_COMPLETION { completionSummary() + if (hook_url) { + imNotification(summary_params) + } + if (input_type == 'sra') { sraCurateSamplesheetWarn() } else if (input_type == 'synapse') { From d1e1bc67a12562bb86f01801cf15e06d61f64282 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 11 Oct 2023 16:16:36 +0200 Subject: [PATCH 128/175] EC lint --- main.nf | 2 +- workflows/sra/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 6d3ea228..bf39d7ea 100644 --- a/main.nf +++ b/main.nf @@ -29,7 +29,7 @@ workflow NFCORE_FETCHNGS { ids // channel: database ids read in from --input main: - + ch_versions = Channel.empty() // diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index a8f54646..ddac096d 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -96,7 +96,7 @@ workflow SRA { // Isolate FASTQ channel which will be added to emit block fastq_files .mix(SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads) - .map { + .map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() From 770de1b7404b40a4f86f3198cbad0f9eff9ca6d8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 11 Oct 2023 16:17:06 +0200 Subject: [PATCH 129/175] update nf-core modules --- .nf-core.yml | 5 + modules.json | 6 +- .../dumpsoftwareversions/tests/main.nf.test | 38 ++++++ .../tests/main.nf.test.snap | 27 +++++ .../dumpsoftwareversions/tests/tags.yml | 2 + .../sratools/fasterqdump/tests/main.nf.test | 69 +++++++++++ .../fasterqdump/tests/main.nf.test.snap | 70 +++++++++++ .../sratools/fasterqdump/tests/tags.yml | 2 + .../sratools/prefetch/tests/main.nf.test | 53 +++++++++ .../sratools/prefetch/tests/main.nf.test.snap | 110 ++++++++++++++++++ .../nf-core/sratools/prefetch/tests/tags.yml | 2 + workflows/sra/tests/main.nf.test | 6 + .../sra_custom_ena_metadata_fields.nf.test | 6 + .../tests/sra_force_sratools_download.nf.test | 6 + .../sra_nf_core_pipeline_atacseq.nf.test | 6 + .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 6 + .../sra_nf_core_pipeline_taxprofiler.nf.test | 6 + .../sra_nf_core_pipeline_viralrecon.nf.test | 6 + .../sra/tests/sra_skip_fastq_download.nf.test | 6 + workflows/sra/tests/tags.yml | 40 ------- 20 files changed, 429 insertions(+), 43 deletions(-) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml create mode 100644 modules/nf-core/sratools/fasterqdump/tests/main.nf.test create mode 100644 modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap create mode 100644 modules/nf-core/sratools/fasterqdump/tests/tags.yml create mode 100644 modules/nf-core/sratools/prefetch/tests/main.nf.test create mode 100644 modules/nf-core/sratools/prefetch/tests/main.nf.test.snap create mode 100644 modules/nf-core/sratools/prefetch/tests/tags.yml diff --git a/.nf-core.yml b/.nf-core.yml index bb27a4e9..0e89cae9 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -4,9 +4,14 @@ lint: files_exist: - .github/workflows/awsfulltest.yml - .github/workflows/awstest.yml + - assets/multiqc_config.yml - conf/igenomes.config - conf/modules.config + - lib/NfcoreTemplate.groovy + - lib/Utils.groovy - lib/WorkflowFetchngs.groovy + - lib/WorkflowMain.groovy + - lib/nfcore_external_java_deps.jar files_unchanged: - .gitattributes - .gitignore diff --git a/modules.json b/modules.json index 6dd402db..d629089b 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", + "git_sha": "1526dc37227a1101bdca25339337362e187a6b3b", "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { @@ -17,12 +17,12 @@ }, "sratools/fasterqdump": { "branch": "master", - "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc", + "git_sha": "b4d743f1bb8d92eb129a5925a9211beb689be625", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/prefetch": { "branch": "master", - "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc", + "git_sha": "096ea8a4db569cc680ada4105e1d313cc56329c8", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..73027efc --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "modules/nf-core/custom/dumpsoftwareversions/main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + tag "modules_nfcore" + + test("Should run without failures") { + setup { + run("FASTQC") { + script "modules/nf-core/fastqc/main.nf" + process { + """ + input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]) + """ + } + } + } + + when { + process { + """ + input[0] = FASTQC.out.versions + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..7398cf5c --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "software_versions.yml:md5,252b721b2ad1475301c9d778c7ce8db2" + ], + "1": [ + "software_versions_mqc.yml:md5,70324befa5d37dd5317190017d53e6dd" + ], + "2": [ + "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + ], + "mqc_yml": [ + "software_versions_mqc.yml:md5,70324befa5d37dd5317190017d53e6dd" + ], + "versions": [ + "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + ], + "yml": [ + "software_versions.yml:md5,252b721b2ad1475301c9d778c7ce8db2" + ] + } + ], + "timestamp": "2023-10-11T15:13:35.246649" + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test new file mode 100644 index 00000000..7da3af20 --- /dev/null +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test @@ -0,0 +1,69 @@ +nextflow_process { + name "Test Process SRATOOLS_FASTERQDUMP" + script "modules/nf-core/sratools/fasterqdump/main.nf" + process "SRATOOLS_FASTERQDUMP" + tag "sratools/fasterqdump" + tag "modules_nfcore" + + test("Single-end") { + + setup { + run("UNTAR") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]) + """ + } + } + } + + when { + process { + """ + input[0] = UNTAR.out.untar.collect{ meta, files -> files }.map{ files -> [ [ id:'test_single_end', single_end:true ], files]} + input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true) + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Paired-end") { + + setup { + run("UNTAR") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]) + """ + } + } + } + + when { + process { + """ + input[0] = UNTAR.out.untar.collect{ meta, files -> files }.map{ files -> [ [ id:'test_paired_end', single_end:false ], files]} + input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true) + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap new file mode 100644 index 00000000..d3bf90f7 --- /dev/null +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap @@ -0,0 +1,70 @@ +{ + "Single-end": { + "content": [ + { + "0": [ + [ + { + "id": "test_single_end", + "single_end": true + }, + "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" + ] + ], + "1": [ + "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + ], + "reads": [ + [ + { + "id": "test_single_end", + "single_end": true + }, + "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" + ] + ], + "versions": [ + "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + ] + } + ], + "timestamp": "2023-10-10T18:11:12.87053" + }, + "Paired-end": { + "content": [ + { + "0": [ + [ + { + "id": "test_paired_end", + "single_end": false + }, + [ + "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6", + "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e" + ] + ] + ], + "1": [ + "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + ], + "reads": [ + [ + { + "id": "test_paired_end", + "single_end": false + }, + [ + "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6", + "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e" + ] + ] + ], + "versions": [ + "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + ] + } + ], + "timestamp": "2023-10-10T18:11:50.928006" + } +} \ No newline at end of file diff --git a/modules/nf-core/sratools/fasterqdump/tests/tags.yml b/modules/nf-core/sratools/fasterqdump/tests/tags.yml new file mode 100644 index 00000000..5d1ddcb3 --- /dev/null +++ b/modules/nf-core/sratools/fasterqdump/tests/tags.yml @@ -0,0 +1,2 @@ +sratools/fasterqdump: + - modules/nf-core/sratools/fasterqdump/** diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test new file mode 100644 index 00000000..1234a82b --- /dev/null +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test @@ -0,0 +1,53 @@ +nextflow_process { + name "Test Process SRATOOLS_PREFETCH" + script "modules/nf-core/sratools/prefetch/main.nf" + process "SRATOOLS_PREFETCH" + tag "sratools/prefetch" + tag "modules_nfcore" + + test("sratools/prefetch") { + + when { + params { + outdir = "output" + } + process { + """ + input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ]) + input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true) + input[2] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process).match() } + ) + } + } + + test("sratools/prefetch with sralite") { + + when { + params { + outdir = "output" + } + process { + """ + input[0] = Channel.of([ [ id:'test', single_end:false ], 'SRR1170046' ]) + input[1] = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true) + input[2] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process).match() } + ) + } + } +} diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap new file mode 100644 index 00000000..95ea067f --- /dev/null +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap @@ -0,0 +1,110 @@ +{ + "sratools/prefetch with sralite": { + "content": [ + { + "stderr": [ + + ], + "errorReport": null, + "exitStatus": 0, + "out": { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" + ] + ] + ], + "1": [ + "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" + ], + "sra": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" + ] + ] + ], + "versions": [ + "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" + ] + }, + "failed": false, + "stdout": [ + + ], + "errorMessage": null, + "trace": { + "tasksFailed": 0, + "tasksCount": 1, + "tasksSucceeded": 1 + }, + "name": "SRATOOLS_PREFETCH", + "success": true + } + ], + "timestamp": "2023-10-10T15:26:45.715617" + }, + "sratools/prefetch": { + "content": [ + { + "stderr": [ + + ], + "errorReport": null, + "exitStatus": 0, + "out": { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" + ] + ] + ], + "1": [ + "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" + ], + "sra": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" + ] + ] + ], + "versions": [ + "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" + ] + }, + "failed": false, + "stdout": [ + + ], + "errorMessage": null, + "trace": { + "tasksFailed": 0, + "tasksCount": 1, + "tasksSucceeded": 1 + }, + "name": "SRATOOLS_PREFETCH", + "success": true + } + ], + "timestamp": "2023-10-10T09:58:01.781848" + } +} \ No newline at end of file diff --git a/modules/nf-core/sratools/prefetch/tests/tags.yml b/modules/nf-core/sratools/prefetch/tests/tags.yml new file mode 100644 index 00000000..52110bfd --- /dev/null +++ b/modules/nf-core/sratools/prefetch/tests/tags.yml @@ -0,0 +1,2 @@ +sratools/prefetch: + - modules/nf-core/sratools/prefetch/** diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index b525bec5..dcf67105 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -3,6 +3,12 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "workflows/sra/main.nf" workflow "SRA" + tag "multiqc_mappings_config" + tag "sra_fastq_ftp" + tag "sra_ids_to_runinfo" + tag "sra_merge_samplesheet" + tag "sra_runinfo_to_ftp" + tag "sra_to_samplesheet" tag "workflows" tag "workflows_sra" tag "sra_default_parameters" diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 7c9df9d9..04a60471 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -3,6 +3,12 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "workflows/sra/main.nf" workflow "SRA" + tag "multiqc_mappings_config" + tag "sra_fastq_ftp" + tag "sra_ids_to_runinfo" + tag "sra_merge_samplesheet" + tag "sra_runinfo_to_ftp" + tag "sra_to_samplesheet" tag "workflows" tag "workflows_sra" tag "sra_custom_ena_metadata_fields" diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 2548689d..c669af8d 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -3,6 +3,12 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "workflows/sra/main.nf" workflow "SRA" + tag "multiqc_mappings_config" + tag "sra_fastq_ftp" + tag "sra_ids_to_runinfo" + tag "sra_merge_samplesheet" + tag "sra_runinfo_to_ftp" + tag "sra_to_samplesheet" tag "workflows" tag "workflows_sra" tag "sra_force_sratools_download" diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index ad60725c..e88e5f63 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -3,6 +3,12 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "workflows/sra/main.nf" workflow "SRA" + tag "multiqc_mappings_config" + tag "sra_fastq_ftp" + tag "sra_ids_to_runinfo" + tag "sra_merge_samplesheet" + tag "sra_runinfo_to_ftp" + tag "sra_to_samplesheet" tag "workflows" tag "workflows_sra" tag "sra_nf_core_pipeline_atacseq" diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 993590ff..63c871ca 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -3,6 +3,12 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "workflows/sra/main.nf" workflow "SRA" + tag "multiqc_mappings_config" + tag "sra_fastq_ftp" + tag "sra_ids_to_runinfo" + tag "sra_merge_samplesheet" + tag "sra_runinfo_to_ftp" + tag "sra_to_samplesheet" tag "workflows" tag "workflows_sra" tag "sra_nf_core_pipeline_rnaseq" diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index a5e69da1..15a31848 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -3,6 +3,12 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "workflows/sra/main.nf" workflow "SRA" + tag "multiqc_mappings_config" + tag "sra_fastq_ftp" + tag "sra_ids_to_runinfo" + tag "sra_merge_samplesheet" + tag "sra_runinfo_to_ftp" + tag "sra_to_samplesheet" tag "workflows" tag "workflows_sra" tag "sra_nf_core_pipeline_taxprofiler" diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index f64cf92e..4c11d571 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -3,6 +3,12 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "workflows/sra/main.nf" workflow "SRA" + tag "multiqc_mappings_config" + tag "sra_fastq_ftp" + tag "sra_ids_to_runinfo" + tag "sra_merge_samplesheet" + tag "sra_runinfo_to_ftp" + tag "sra_to_samplesheet" tag "workflows" tag "workflows_sra" tag "sra_nf_core_pipeline_viralrecon" diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index aa290c68..8cb68641 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -3,6 +3,12 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "workflows/sra/main.nf" workflow "SRA" + tag "multiqc_mappings_config" + tag "sra_fastq_ftp" + tag "sra_ids_to_runinfo" + tag "sra_merge_samplesheet" + tag "sra_runinfo_to_ftp" + tag "sra_to_samplesheet" tag "workflows" tag "workflows_sra" tag "sra_skip_fastq_download" diff --git a/workflows/sra/tests/tags.yml b/workflows/sra/tests/tags.yml index 52c3e591..ae41e37d 100644 --- a/workflows/sra/tests/tags.yml +++ b/workflows/sra/tests/tags.yml @@ -1,56 +1,16 @@ sra_custom_ena_metadata_fields: - - modules/local/sra_ids_to_runinfo/** - - modules/local/sra_runinfo_to_ftp/** - - modules/local/sra_fastq_ftp/** - - modules/local/sra_to_samplesheet/** - - modules/local/sra_merge_samplesheet/** - workflows/sra/** sra_default_parameters: - - modules/local/sra_ids_to_runinfo/** - - modules/local/sra_runinfo_to_ftp/** - - modules/local/sra_fastq_ftp/** - - modules/local/sra_to_samplesheet/** - - modules/local/sra_merge_samplesheet/** - workflows/sra/** sra_force_sratools_download: - - modules/local/sra_ids_to_runinfo/** - - modules/local/sra_runinfo_to_ftp/** - - modules/local/sra_fastq_ftp/** - - modules/local/sra_to_samplesheet/** - - modules/local/sra_merge_samplesheet/** - workflows/sra/** sra_nf_core_pipeline_atacseq: - - modules/local/sra_ids_to_runinfo/** - - modules/local/sra_runinfo_to_ftp/** - - modules/local/sra_fastq_ftp/** - - modules/local/sra_to_samplesheet/** - - modules/local/sra_merge_samplesheet/** - workflows/sra/** sra_nf_core_pipeline_rnaseq: - - modules/local/sra_ids_to_runinfo/** - - modules/local/sra_runinfo_to_ftp/** - - modules/local/sra_fastq_ftp/** - - modules/local/sra_to_samplesheet/** - - modules/local/sra_merge_samplesheet/** - workflows/sra/** sra_nf_core_pipeline_taxprofiler: - - modules/local/sra_ids_to_runinfo/** - - modules/local/sra_runinfo_to_ftp/** - - modules/local/sra_fastq_ftp/** - - modules/local/sra_to_samplesheet/** - - modules/local/sra_merge_samplesheet/** - workflows/sra/** sra_nf_core_pipeline_viralrecon: - - modules/local/sra_ids_to_runinfo/** - - modules/local/sra_runinfo_to_ftp/** - - modules/local/sra_fastq_ftp/** - - modules/local/sra_to_samplesheet/** - - modules/local/sra_merge_samplesheet/** - workflows/sra/** sra_skip_fastq_download: - - modules/local/sra_ids_to_runinfo/** - - modules/local/sra_runinfo_to_ftp/** - - modules/local/sra_fastq_ftp/** - - modules/local/sra_to_samplesheet/** - - modules/local/sra_merge_samplesheet/** - workflows/sra/** From 6002c61f880b28bfcb817d9833854a141713d595 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 11 Oct 2023 16:20:27 +0200 Subject: [PATCH 130/175] update nf-test version --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 436b61a5..70f7f815 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.0" + NFTEST_VER: "0.8.1" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From f85e0321d27fa8e759a19ed39d9347883bd2feab Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:04:40 +0100 Subject: [PATCH 131/175] Use relative paths for main script location for nf-test --- modules/local/multiqc_mappings_config/tests/main.nf.test | 2 +- modules/local/sra_fastq_ftp/tests/main.nf.test | 2 +- modules/local/sra_ids_to_runinfo/tests/main.nf.test | 2 +- modules/local/sra_merge_samplesheet/tests/main.nf.test | 2 +- modules/local/sra_runinfo_to_ftp/tests/main.nf.test | 2 +- modules/local/sra_to_samplesheet/tests/main.nf.test | 2 +- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +- workflows/sra/tests/sra_force_sratools_download.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +- workflows/sra/tests/sra_skip_fastq_download.nf.test | 2 +- 14 files changed, 14 insertions(+), 14 deletions(-) diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index 3bf79537..75356197 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: MULTIQC_MAPPINGS_CONFIG" - script "modules/local/multiqc_mappings_config/main.nf" + script "../main.nf" process "MULTIQC_MAPPINGS_CONFIG" tag "modules" tag "modules_local" diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index 7892d156..ab846e5d 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_FASTQ_FTP" - script "modules/local/sra_fastq_ftp/main.nf" + script "../main.nf" process "SRA_FASTQ_FTP" tag "modules" tag "modules_local" diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test index f8a44086..087f9069 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_IDS_TO_RUNINFO" - script "modules/local/sra_ids_to_runinfo/main.nf" + script "../main.nf" process "SRA_IDS_TO_RUNINFO" tag "modules" tag "modules_local" diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test index e37039bd..b7c98622 100644 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_MERGE_SAMPLESHEET" - script "modules/local/sra_merge_samplesheet/main.nf" + script "../main.nf" process "SRA_MERGE_SAMPLESHEET" tag "modules" tag "modules_local" diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test index 1558ff39..3b1405f9 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_RUNINFO_TO_FTP" - script "modules/local/sra_runinfo_to_ftp/main.nf" + script "../main.nf" process "SRA_RUNINFO_TO_FTP" tag "modules" tag "modules_local" diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index b2ec5b11..6094717b 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test process: SRA_TO_SAMPLESHEET" - script "modules/local/sra_to_samplesheet/main.nf" + script "../main.nf" process "SRA_TO_SAMPLESHEET" tag "modules" tag "modules_local" diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index dcf67105..6b459773 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 04a60471..0d0b85df 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index c669af8d..5cd54142 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index e88e5f63..ef069674 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 63c871ca..4eb57027 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 15a31848..019c9af8 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 4c11d571..dce26b16 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 8cb68641..142e8aff 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -1,7 +1,7 @@ nextflow_workflow { name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" + script "../main.nf" workflow "SRA" tag "multiqc_mappings_config" tag "sra_fastq_ftp" From 3776119a8717fc723bd60188124f9a92943713fa Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:05:06 +0100 Subject: [PATCH 132/175] Remove nf-test branch from ci.yml --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 70f7f815..ef127625 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,7 +11,6 @@ on: - master - dev - refactor - - nf-test env: NXF_ANSI_LOG: false From c44000154a7232911c081fa1511639c1ce635dc0 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:14:23 +0100 Subject: [PATCH 133/175] Update CHANGELOG and author contributions --- CHANGELOG.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c500efcc..9264eb59 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unpublished Version / DEV] +### Credits + +Special thanks to the following for their contributions to the release: + +- [Adam Talbot](https://github.com/adamrtalbot) +- [Edmund Miller](https://github.com/Emiller88) +- [Esha Joshi](https://github.com/ejseqera) +- [Harshil Patel](https://github.com/drpatelh) +- [James Fellows Yates](https://github.com/jfy133) +- [Maxime Garcia](https://github.com/maxulysse) +- [Rob Syme](https://github.com/robsyme) +- [Sateesh Peri](https://github.com/sateeshperi) + +Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. + +### Enhancements & fixes + +- [PR #XXX](https://github.com/nf-core/fetchngs/pull/XXX) - Use nf-test for all pipeline testing + ### Enhancements & fixes ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08 @@ -14,8 +33,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 Special thanks to the following for their contributions to the release: - [Adam Talbot](https://github.com/adamrtalbot) +- [Davide Carlson](https://github.com/davidecarlson) - [Harshil Patel](https://github.com/drpatelh) - [Maxime Garcia](https://github.com/maxulysse) +- [MCMandR](https://github.com/MCMandR) - [Rob Syme](https://github.com/robsyme) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. From 46f258fd879870aae381e9db9e6a14e443ad3ef7 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:17:42 +0100 Subject: [PATCH 134/175] Add nf-test citation --- CITATIONS.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CITATIONS.md b/CITATIONS.md index 570e7e5b..482d5600 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -37,7 +37,7 @@ - [Synapse](https://pubmed.ncbi.nlm.nih.gov/24071850/) > Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct;45(10):1121-6. doi: 10.1038/ng.2761. PMID: 24071850; PMCID: PMC3950337. -## Software packaging/containerisation tools +## Software packaging/containerisation/testing tools - [Anaconda](https://anaconda.com) @@ -55,6 +55,8 @@ > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. +- [nf-test](https://code.askimed.com/nf-test) + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. From 025f0ae6bb4807a6c5a688e211845fe6149ee76f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 12 Oct 2023 12:26:38 +0200 Subject: [PATCH 135/175] update custom/dumpsoftwareversions --- modules.json | 2 +- .../dumpsoftwareversions/tests/main.nf.test | 23 +++++++++---------- .../tests/main.nf.test.snap | 10 ++++---- 3 files changed, 17 insertions(+), 18 deletions(-) diff --git a/modules.json b/modules.json index d629089b..87e40abf 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "1526dc37227a1101bdca25339337362e187a6b3b", + "git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0", "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test index 73027efc..d528d3cb 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -9,21 +9,20 @@ nextflow_process { tag "modules_nfcore" test("Should run without failures") { - setup { - run("FASTQC") { - script "modules/nf-core/fastqc/main.nf" - process { - """ - input[0] = Channel.of([ [], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]) - """ - } - } - } - when { process { """ - input[0] = FASTQC.out.versions + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() """ } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap index 7398cf5c..8713b921 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -3,25 +3,25 @@ "content": [ { "0": [ - "software_versions.yml:md5,252b721b2ad1475301c9d778c7ce8db2" + "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" ], "1": [ - "software_versions_mqc.yml:md5,70324befa5d37dd5317190017d53e6dd" + "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" ], "2": [ "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" ], "mqc_yml": [ - "software_versions_mqc.yml:md5,70324befa5d37dd5317190017d53e6dd" + "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" ], "versions": [ "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" ], "yml": [ - "software_versions.yml:md5,252b721b2ad1475301c9d778c7ce8db2" + "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" ] } ], - "timestamp": "2023-10-11T15:13:35.246649" + "timestamp": "2023-10-11T17:10:02.930699" } } From f65a861e36aa2238295219572480f64bc1249554 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 11:38:23 +0100 Subject: [PATCH 136/175] Remove workflows/nextflow.config --- nextflow.config | 17 ++++++++++------- workflows/nextflow.config | 12 ------------ 2 files changed, 10 insertions(+), 19 deletions(-) delete mode 100644 workflows/nextflow.config diff --git a/nextflow.config b/nextflow.config index 5ad350c9..3589e118 100644 --- a/nextflow.config +++ b/nextflow.config @@ -65,6 +65,16 @@ try { System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } +// Module specific configs +includeConfig './modules/nf-core/custom/dumpsoftwareversions/nextflow.config' + +// Workflow specific configs +if (params.input_type == 'sra') { + includeConfig './workflows/sra/nextflow.config' +} else if (params.input_type == 'synapse') { + includeConfig './workflows/synapse/nextflow.config' +} + // Load nf-core/fetchngs custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! // try { @@ -227,13 +237,6 @@ manifest { doi = 'https://doi.org/10.5281/zenodo.5070524' } -// Module specific configs -// Currently just dumpsoftwareversions -includeConfig 'modules/nf-core/custom/dumpsoftwareversions/nextflow.config' - -// Workflow specific configs -includeConfig 'workflows/nextflow.config' - // Function to ensure that resource requirements don't go beyond // a maximum limit def check_max(obj, type) { diff --git a/workflows/nextflow.config b/workflows/nextflow.config deleted file mode 100644 index d27deb3a..00000000 --- a/workflows/nextflow.config +++ /dev/null @@ -1,12 +0,0 @@ -// Read in specific config relating to workflow. - -switch ( params.input_type ) { - case "sra": - includeConfig './sra/nextflow.config' - break - case "synapse": - includeConfig './synapse/nextflow.config' - break - default: - break -} \ No newline at end of file From 67f05771f286f141e15d628d39aede3c08087a59 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 12 Oct 2023 15:45:39 +0200 Subject: [PATCH 137/175] same install --- .github/workflows/ci.yml | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 70f7f815..16f6e1c8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -76,9 +76,19 @@ jobs: with: version: "${{ matrix.NXF_VER }}" + - name: Cache nf-test installation + id: cache-software + uses: actions/cache@v3 + with: + path: | + /usr/local/bin/nf-test + /home/runner/.nf-test/nf-test.jar + key: ${{ runner.os }}-${{ env.NF_TEST_VER }}-nftest + - name: Install nf-test + if: steps.cache-software.outputs.cache-hit != 'true' run: | - wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER + wget -qO- https://code.askimed.com/install/nf-test | bash sudo mv nf-test /usr/local/bin/ - name: Run nf-test From 92e75880697e99fed3df6e1290380c268683e409 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 12 Oct 2023 15:47:54 +0200 Subject: [PATCH 138/175] fix env --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 16f6e1c8..2dd4d4e7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -83,7 +83,7 @@ jobs: path: | /usr/local/bin/nf-test /home/runner/.nf-test/nf-test.jar - key: ${{ runner.os }}-${{ env.NF_TEST_VER }}-nftest + key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest - name: Install nf-test if: steps.cache-software.outputs.cache-hit != 'true' From 803c473e82be0b7f9d46749aee603f2347c528e8 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 18:43:49 +0100 Subject: [PATCH 139/175] Add nf-test authors to credits for release --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9264eb59..9fbb2013 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,10 +13,12 @@ Special thanks to the following for their contributions to the release: - [Edmund Miller](https://github.com/Emiller88) - [Esha Joshi](https://github.com/ejseqera) - [Harshil Patel](https://github.com/drpatelh) +- [Lukas Forer](https://github.com/lukfor) - [James Fellows Yates](https://github.com/jfy133) - [Maxime Garcia](https://github.com/maxulysse) - [Rob Syme](https://github.com/robsyme) - [Sateesh Peri](https://github.com/sateeshperi) +- [Sebastian Schönherr](https://github.com/seppinho) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. From 9eebe984d5cf799a5c9361a84f1cad71fc7f4354 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 13 Oct 2023 09:43:49 +0100 Subject: [PATCH 140/175] Re-order tags in workflow nf-test files --- workflows/sra/tests/main.nf.test | 4 ++-- workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 4 ++-- workflows/sra/tests/sra_force_sratools_download.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 4 ++-- workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 4 ++-- workflows/sra/tests/sra_skip_fastq_download.nf.test | 4 ++-- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 6b459773..1595f94d 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_default_parameters" test("Parameters: default") { diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 0d0b85df..ca3d5bd0 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_custom_ena_metadata_fields" test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 5cd54142..f8f6ff5c 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_force_sratools_download" test("Parameters: --force_sratools_download") { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index ef069674..5a854533 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_nf_core_pipeline_atacseq" test("Parameters: --nf_core_pipeline atacseq") { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 4eb57027..aeb06857 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_nf_core_pipeline_rnaseq" test("Parameters: --nf_core_pipeline rnaseq") { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 019c9af8..c460ffbd 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_nf_core_pipeline_taxprofiler" test("Parameters: --nf_core_pipeline taxprofiler") { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index dce26b16..f90d8958 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_nf_core_pipeline_viralrecon" test("Parameters: --nf_core_pipeline viralrecon") { diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 142e8aff..8d21a3d9 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -3,14 +3,14 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" + tag "workflows" + tag "workflows_sra" tag "multiqc_mappings_config" tag "sra_fastq_ftp" tag "sra_ids_to_runinfo" tag "sra_merge_samplesheet" tag "sra_runinfo_to_ftp" tag "sra_to_samplesheet" - tag "workflows" - tag "workflows_sra" tag "sra_skip_fastq_download" test("Parameters: --skip_fastq_download") { From f06790c3dec3eb4a8aea62b3290361ffae33375b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 10:45:36 +0200 Subject: [PATCH 141/175] add pipeline level tests --- conf/test.config | 2 +- tests/main.nf.test | 27 +++++++++++++++++++++++++++ tests/sra_ids_test.csv | 7 +++++++ 3 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 tests/main.nf.test create mode 100644 tests/sra_ids_test.csv diff --git a/conf/test.config b/conf/test.config index cb77f578..67291b47 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,7 +20,7 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv' + input = 'tests/sra_ids_test.csv' validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data' } diff --git a/tests/main.nf.test b/tests/main.nf.test new file mode 100644 index 00000000..7bf19f34 --- /dev/null +++ b/tests/main.nf.test @@ -0,0 +1,27 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + + test("Run with profile test") { + + when { + params { + outdir = "results" + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' + input = "$projectDir/tests/sra_ids_test.csv" + validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data' + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + +} diff --git a/tests/sra_ids_test.csv b/tests/sra_ids_test.csv new file mode 100644 index 00000000..ec8b5cc9 --- /dev/null +++ b/tests/sra_ids_test.csv @@ -0,0 +1,7 @@ +SRR9984183 +SRR13191702 +ERR1160846 +SRR12848126 +SRR14593545 +SRR14709033 +GSE214215 From 6f94f654f3568a93a4dc319bb8e620cca1c50a9e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 11:07:14 +0200 Subject: [PATCH 142/175] add tags --- tests/tags.yml | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 tests/tags.yml diff --git a/tests/tags.yml b/tests/tags.yml new file mode 100644 index 00000000..3a1868da --- /dev/null +++ b/tests/tags.yml @@ -0,0 +1,4 @@ +pipeline_fetchngs: + - **.nf + - **.config + - **.nf.test From e9917d81b017d73d7c929ff6fcbadeff3aec018b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 11:17:19 +0200 Subject: [PATCH 143/175] update tags --- tests/tags.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/tags.yml b/tests/tags.yml index 3a1868da..5b091f8e 100644 --- a/tests/tags.yml +++ b/tests/tags.yml @@ -1,4 +1,4 @@ pipeline_fetchngs: - - **.nf - - **.config - - **.nf.test + - "**.nf" + - "**.config" + - "**.nf.test" From 91d59aa6251cb68a695d48901ee5e6fb4e72acad Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 11:37:48 +0200 Subject: [PATCH 144/175] use proper tag --- tests/main.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/main.nf.test b/tests/main.nf.test index 7bf19f34..ac05aea9 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test pipeline" script "../main.nf" tag "pipeline" + tag "pipeline_fetchngs" test("Run with profile test") { From 796728a52184426ba3c8a5761d16a8b7b321b5ae Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 11:38:44 +0200 Subject: [PATCH 145/175] extends files to trigger test --- tests/tags.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/tags.yml b/tests/tags.yml index 5b091f8e..80e5fd75 100644 --- a/tests/tags.yml +++ b/tests/tags.yml @@ -2,3 +2,4 @@ pipeline_fetchngs: - "**.nf" - "**.config" - "**.nf.test" + - "**.json" From 8b6570b3a1cf7575721f51dead316b591c66d7e5 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 13 Oct 2023 12:23:23 +0200 Subject: [PATCH 146/175] Update conf/test.config Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index 67291b47..c09a571c 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,7 +20,7 @@ params { max_time = '6.h' // Input data - input = 'tests/sra_ids_test.csv' + input = '${projectDir}/tests/sra_ids_test.csv' validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data' } From 4ec46062e22c5b1acdeea67258ad64d3548f60fc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 13:36:45 +0200 Subject: [PATCH 147/175] use same IDs as profile test --- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +- workflows/sra/tests/sra_force_sratools_download.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +- workflows/sra/tests/sra_skip_fastq_download.nf.test | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index dcf67105..af916f4c 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 04a60471..0fdb67f3 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index c669af8d..7958a1ed 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index e88e5f63..dfccf891 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 63c871ca..fd092bcd 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 15a31848..a41d2b7a 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 4c11d571..c052d915 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 8cb68641..04eb3dd7 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { From c75c1d05dff6a6455de4a1a192bbe2c88825db43 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 13:56:15 +0200 Subject: [PATCH 148/175] update snap --- workflows/sra/tests/main.nf.test.snap | 14 +++++++------- .../sra_custom_ena_metadata_fields.nf.test.snap | 14 +++++++------- .../tests/sra_force_sratools_download.nf.test.snap | 14 +++++++------- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 14 +++++++------- .../tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 14 +++++++------- .../sra_nf_core_pipeline_taxprofiler.nf.test.snap | 14 +++++++------- .../sra_nf_core_pipeline_viralrecon.nf.test.snap | 14 +++++++------- .../sra/tests/sra_skip_fastq_download.nf.test.snap | 14 +++++++------- 8 files changed, 56 insertions(+), 56 deletions(-) diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index d53f3de2..4ba15917 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" + "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac" ], "2": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "3": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" + "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-09T11:10:06.701286" + "timestamp": "2023-10-13T13:45:55.621951" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 143375ac..5e98f3b1 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5" + "samplesheet.csv:md5,4ea86d2a38bf25d025331afd1925a138" ], "2": [ - "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" + "id_mappings.csv:md5,e581a9117ed2cc8e98e65c25fe7f34aa" ], "3": [ [ - "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235", + "multiqc_config.yml:md5,0f18d574c7ddfa08cf444a593cb91cde", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" + "id_mappings.csv:md5,e581a9117ed2cc8e98e65c25fe7f34aa" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235", + "multiqc_config.yml:md5,0f18d574c7ddfa08cf444a593cb91cde", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5" + "samplesheet.csv:md5,4ea86d2a38bf25d025331afd1925a138" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-06T12:10:32.762201" + "timestamp": "2023-10-13T13:41:56.570144" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index a22fad41..1c92c75d 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,f582a7cf6b4a507e3ccbd2ebd134bd26" + "samplesheet.csv:md5,461dfaa7b95f84210840347ef8cc93c2" ], "2": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "3": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -28,16 +28,16 @@ ], "mappings": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,f582a7cf6b4a507e3ccbd2ebd134bd26" + "samplesheet.csv:md5,461dfaa7b95f84210840347ef8cc93c2" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2023-10-09T12:31:35.173406" + "timestamp": "2023-10-13T13:51:26.617172" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 3e26ff24..cabe296e 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe" + "samplesheet.csv:md5,0deebc93328dcbb63762aa91d4fc9f35" ], "2": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "3": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe" + "samplesheet.csv:md5,0deebc93328dcbb63762aa91d4fc9f35" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-09T11:48:46.177797" + "timestamp": "2023-10-13T13:37:42.486986" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index a0c20a40..111fe537 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767" + "samplesheet.csv:md5,e20d0858b2ff04a62d50274a2527b913" ], "2": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "3": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767" + "samplesheet.csv:md5,e20d0858b2ff04a62d50274a2527b913" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-06T12:14:02.500312" + "timestamp": "2023-10-13T13:43:56.980991" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index d9d6ddee..14c38837 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc" + "samplesheet.csv:md5,c781b226b9aac812c1d38881145a74d6" ], "2": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "3": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc" + "samplesheet.csv:md5,c781b226b9aac812c1d38881145a74d6" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-06T12:07:01.184728" + "timestamp": "2023-10-13T13:39:55.31037" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index cacb42cc..d26dd1cc 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" + "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac" ], "2": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "3": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" + "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-09T11:44:49.759545" + "timestamp": "2023-10-13T13:35:41.371352" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index c137d853..f0bac51f 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b" + "samplesheet.csv:md5,23d39235ed39f69cb8333322de77ed26" ], "2": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "3": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -27,16 +27,16 @@ ], "mappings": [ - "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" + "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b" + "samplesheet.csv:md5,23d39235ed39f69cb8333322de77ed26" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -46,6 +46,6 @@ ] } ], - "timestamp": "2023-10-06T12:18:48.477246" + "timestamp": "2023-10-13T13:46:11.136377" } } \ No newline at end of file From 0f6cbd4721c854283562c7f894ea3afe877e2798 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 14:36:20 +0200 Subject: [PATCH 149/175] add file for sratools/prefetch --- conf/test_data.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/test_data.config b/conf/test_data.config index 42d3d818..68e84262 100644 --- a/conf/test_data.config +++ b/conf/test_data.config @@ -24,6 +24,11 @@ params { } test_data { + 'generic' { + 'config' { + ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg" + } + } 'modules_local' { multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv" sra_merge_samplesheet_samplesheets = merge_samplesheet_urls From 1520425356b02d673680a181f64907114c33f333 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 15:00:35 +0200 Subject: [PATCH 150/175] update modules --- modules.json | 10 +- .../dumpsoftwareversions/tests/main.nf.test | 5 +- .../sratoolsncbisettings/tests/main.nf.test | 114 +++++++++++++++ .../tests/main.nf.test.snap | 18 +++ .../tests/nextflow.config | 16 +++ .../sratools/fasterqdump/tests/main.nf.test | 5 +- .../sratools/prefetch/tests/main.nf.test | 9 +- .../sratools/prefetch/tests/main.nf.test.snap | 130 +++++++----------- .../tests/main.nf.test | 37 +++++ .../tests/main.nf.test.snap | 57 ++++++++ 10 files changed, 304 insertions(+), 97 deletions(-) create mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test create mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap diff --git a/modules.json b/modules.json index 87e40abf..b826fae6 100644 --- a/modules.json +++ b/modules.json @@ -7,22 +7,22 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0", + "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/fasterqdump": { "branch": "master", - "git_sha": "b4d743f1bb8d92eb129a5925a9211beb689be625", + "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/prefetch": { "branch": "master", - "git_sha": "096ea8a4db569cc680ada4105e1d313cc56329c8", + "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] } } @@ -31,7 +31,7 @@ "nf-core": { "fastq_download_prefetch_fasterqdump_sratools": { "branch": "master", - "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test index d528d3cb..eec1db10 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -1,12 +1,13 @@ nextflow_process { name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "modules/nf-core/custom/dumpsoftwareversions/main.nf" + script "../main.nf" process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" tag "custom" tag "dumpsoftwareversions" tag "custom/dumpsoftwareversions" - tag "modules_nfcore" test("Should run without failures") { when { diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test new file mode 100644 index 00000000..ec4a7797 --- /dev/null +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test @@ -0,0 +1,114 @@ +nextflow_process { + + name "Test Process CUSTOM_SRATOOLSNCBISETTINGS" + script "../main.nf" + process "CUSTOM_SRATOOLSNCBISETTINGS" + config "modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "custom/sratoolsncbisettings" + + test("Should run without failures") { + + when { + params { + settings_path = '/tmp/.ncbi' + settings_file = "${params.settings_path}/user-settings.mkfg" + } + + process { + """ + file(params.settings_path).mkdirs() + def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true) + settings.copyTo(params.settings_file) + """ + } + } + + then { + assert process.success + assert snapshot( + process.out.versions + ).match() + + with(process.out.ncbi_settings) { + assert path(get(0)).readLines().any { it.contains('/LIBS/GUID') } + assert path(get(0)).readLines().any { it.contains('/libs/cloud/report_instance_identity') } + } + } + + } + + test("Should fail") { + + when { + params { + settings_path = '/tmp/.ncbi' + settings_file = "${params.settings_path}/user-settings.mkfg" + } + + process { + """ + file(params.settings_path).mkdirs() + def settings = file(params.settings_file) + settings.text = ''' + ## auto-generated configuration file - DO NOT EDIT ## + config/default = "false" + /repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi" + /repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi" + /repository/user/ad/public/apps/file/volumes/flatAd = "." + /repository/user/ad/public/apps/refseq/volumes/refseqAd = "." + /repository/user/ad/public/apps/sra/volumes/sraAd = "." + /repository/user/ad/public/apps/sraPileup/volumes/ad = "." + /repository/user/ad/public/apps/sraRealign/volumes/ad = "." + /repository/user/ad/public/apps/wgs/volumes/wgsAd = "." + /repository/user/ad/public/root = "." + /repository/user/default-path = "/root/ncbi" + '''.stripIndent() + """ + } + } + + then { + assert process.failed + assert snapshot( + process.out.versions + ).match() + assert process.stdout.any { it.contains('Command error:') } + assert process.stdout.any { it.contains('missing the required entries') } + assert process.stdout.any { it.contains('/LIBS/GUID') } + assert process.stdout.any { it.contains('/libs/cloud/report_instance_identity') } + } + + } + + test("Should run with nonexisting") { + + when { + params { + settings_path = '/tmp/.ncbi' + settings_file = "${params.settings_path}/user-settings.mkfg" + } + + process { + """ + def settings = file(params.settings_file) + settings.delete() + """ + } + } + + then { + assert process.success + assert snapshot(process.out.versions).match() + + with(process.out.ncbi_settings) { + { assert path(get(0)).readLines().any { it.contains('/LIBS/GUID') } } + { assert path(get(0)).readLines().any { it.contains('/libs/cloud/report_instance_identity') } } + } + } + + } + +} diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap new file mode 100644 index 00000000..edb3b351 --- /dev/null +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap @@ -0,0 +1,18 @@ +{ + "Should run with nonexisting": { + "content": [ + [ + "versions.yml:md5,fec13b593c3b42ddd38f2fc77df25b70" + ] + ], + "timestamp": "2023-10-12T12:24:24.023849" + }, + "Should run without failures": { + "content": [ + [ + "versions.yml:md5,fec13b593c3b42ddd38f2fc77df25b70" + ] + ], + "timestamp": "2023-10-12T10:40:51.717351" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config new file mode 100644 index 00000000..c4a96e94 --- /dev/null +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config @@ -0,0 +1,16 @@ +params.settings_path = '/tmp/.ncbi' +params.settings_file = "${params.settings_path}/user-settings.mkfg" + +env.NCBI_SETTINGS = params.settings_file + +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + withName: CUSTOM_SRATOOLSNCBISETTINGS { + containerOptions = { + (workflow.containerEngine == 'singularity') ? + "-B ${params.settings_path}:${params.settings_path}" : + "-v ${params.settings_path}:${params.settings_path}" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test index 7da3af20..ee4c5844 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test @@ -1,9 +1,10 @@ nextflow_process { name "Test Process SRATOOLS_FASTERQDUMP" - script "modules/nf-core/sratools/fasterqdump/main.nf" + script "../main.nf" process "SRATOOLS_FASTERQDUMP" - tag "sratools/fasterqdump" + tag "modules" tag "modules_nfcore" + tag "sratools/fasterqdump" test("Single-end") { diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test index 1234a82b..fcf4036d 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test @@ -1,9 +1,10 @@ nextflow_process { name "Test Process SRATOOLS_PREFETCH" - script "modules/nf-core/sratools/prefetch/main.nf" + script "../main.nf" process "SRATOOLS_PREFETCH" - tag "sratools/prefetch" + tag "modules" tag "modules_nfcore" + tag "sratools/prefetch" test("sratools/prefetch") { @@ -23,7 +24,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process).match() } + { assert snapshot(process.out).match() } ) } } @@ -46,7 +47,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process).match() } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap index 95ea067f..ab1d2088 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap @@ -2,109 +2,71 @@ "sratools/prefetch with sralite": { "content": [ { - "stderr": [ - - ], - "errorReport": null, - "exitStatus": 0, - "out": { - "0": [ + "0": [ + [ + { + "id": "test", + "single_end": false + }, [ - { - "id": "test", - "single_end": false - }, - [ - "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" - ] + "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" ] - ], - "1": [ - "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" - ], - "sra": [ + ] + ], + "1": [ + "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" + ], + "sra": [ + [ + { + "id": "test", + "single_end": false + }, [ - { - "id": "test", - "single_end": false - }, - [ - "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" - ] + "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" ] - ], - "versions": [ - "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" ] - }, - "failed": false, - "stdout": [ - ], - "errorMessage": null, - "trace": { - "tasksFailed": 0, - "tasksCount": 1, - "tasksSucceeded": 1 - }, - "name": "SRATOOLS_PREFETCH", - "success": true + "versions": [ + "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" + ] } ], - "timestamp": "2023-10-10T15:26:45.715617" + "timestamp": "2023-10-13T12:11:24.563510389" }, "sratools/prefetch": { "content": [ { - "stderr": [ - - ], - "errorReport": null, - "exitStatus": 0, - "out": { - "0": [ + "0": [ + [ + { + "id": "test", + "single_end": false + }, [ - { - "id": "test", - "single_end": false - }, - [ - "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" - ] + "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" ] - ], - "1": [ - "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" - ], - "sra": [ + ] + ], + "1": [ + "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" + ], + "sra": [ + [ + { + "id": "test", + "single_end": false + }, [ - { - "id": "test", - "single_end": false - }, - [ - "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" - ] + "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" ] - ], - "versions": [ - "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" ] - }, - "failed": false, - "stdout": [ - ], - "errorMessage": null, - "trace": { - "tasksFailed": 0, - "tasksCount": 1, - "tasksSucceeded": 1 - }, - "name": "SRATOOLS_PREFETCH", - "success": true + "versions": [ + "versions.yml:md5,c967dea4135cb75490e1e801c4639efc" + ] } ], - "timestamp": "2023-10-10T09:58:01.781848" + "timestamp": "2023-10-13T12:11:02.75256571" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test new file mode 100644 index 00000000..be18fc3b --- /dev/null +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test @@ -0,0 +1,37 @@ +nextflow_workflow { + + name "Test workflow: fastq_download_prefetch_fasterqdump_sratools/main.nf" + script "../main.nf" + workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS" + tag "subworkflow" + tag "subworkflow_nfcore" + tag "custom/sratoolsncbisettings" + tag "sratools/prefetch" + tag "sratools/fasterqdump" + tag "fastq_download_prefetch_fasterqdump_sratools" + + test("Parameters: default") { + + when { + workflow { + """ + input[0] = Channel.of( + [[ id:'test_single_end', single_end:true ], 'DRR000774'], + [[ id:'test_paired_end', single_end:false ], 'SRR11140744'] + ) + input[1] = [] + """ + } + params { + outdir = "output" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap new file mode 100644 index 00000000..a73679e0 --- /dev/null +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap @@ -0,0 +1,57 @@ +{ + "Parameters: default": { + "content": [ + { + "0": [ + [ + { + "id": "test_paired_end", + "single_end": false + }, + [ + "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6", + "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e" + ] + ], + [ + { + "id": "test_single_end", + "single_end": true + }, + "test_single_end.fastq.gz:md5,19029a1132115b55277a0d79ee089b49" + ] + ], + "1": [ + "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224", + "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db", + "versions.yml:md5,db0e1352064b53c651661f43f2620765" + ], + "reads": [ + [ + { + "id": "test_paired_end", + "single_end": false + }, + [ + "test_paired_end_1.fastq.gz:md5,193809c784a4ea132ab2a253fa4f55b6", + "test_paired_end_2.fastq.gz:md5,3e3b3af3413f50a1685fd7b3f1456d4e" + ] + ], + [ + { + "id": "test_single_end", + "single_end": true + }, + "test_single_end.fastq.gz:md5,19029a1132115b55277a0d79ee089b49" + ] + ], + "versions": [ + "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224", + "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db", + "versions.yml:md5,db0e1352064b53c651661f43f2620765" + ] + } + ], + "timestamp": "2023-10-12T20:09:55.255971" + } +} \ No newline at end of file From a38f6410090a56ee395902bb8c0444f9e156ad05 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 15:18:41 +0200 Subject: [PATCH 151/175] use nextflowpipelineutils from nf-core/modules --- modules.json | 5 + .../local/nf_core_fetchngs_utils/main.nf | 4 +- .../nextflowpipelineutils}/main.nf | 3 + .../nf-core/nextflowpipelineutils/meta.yml | 34 ++++++ .../tests/main.functions.nf.test | 70 ++++++++++++ .../tests/main.functions.nf.test.snap | 12 ++ .../tests/main.workflow.nf.test | 104 ++++++++++++++++++ .../tests/main.workflow.nf.test.snap | 44 ++++++++ .../tests/nextflow.config | 9 ++ 9 files changed, 283 insertions(+), 2 deletions(-) rename subworkflows/{local/nextflow_pipeline_utils => nf-core/nextflowpipelineutils}/main.nf (99%) create mode 100644 subworkflows/nf-core/nextflowpipelineutils/meta.yml create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config diff --git a/modules.json b/modules.json index b826fae6..3cc9d6dd 100644 --- a/modules.json +++ b/modules.json @@ -33,6 +33,11 @@ "branch": "master", "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", "installed_by": ["subworkflows"] + }, + "nextflowpipelineutils": { + "branch": "master", + "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3", + "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index 5cc2162b..fd0e9855 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -9,7 +9,7 @@ */ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../modules/nf-core/custom/dumpsoftwareversions' -include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../nextflow_pipeline_utils' +include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main' include { NF_VALIDATION_PLUGIN_UTILS } from '../nf_validation_plugin_utils' include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils' @@ -49,7 +49,7 @@ workflow PIPELINE_INITIALISATION { // // Check config provided to the pipeline - // + // NF_CORE_PIPELINE_UTILS () // diff --git a/subworkflows/local/nextflow_pipeline_utils/main.nf b/subworkflows/nf-core/nextflowpipelineutils/main.nf similarity index 99% rename from subworkflows/local/nextflow_pipeline_utils/main.nf rename to subworkflows/nf-core/nextflowpipelineutils/main.nf index e56394ed..5cb9af8c 100644 --- a/subworkflows/local/nextflow_pipeline_utils/main.nf +++ b/subworkflows/nf-core/nextflowpipelineutils/main.nf @@ -42,6 +42,9 @@ workflow NEXTFLOW_PIPELINE_UTILS { if (check_conda_channels) { checkCondaChannels() } + + emit: + out = true } /* diff --git a/subworkflows/nf-core/nextflowpipelineutils/meta.yml b/subworkflows/nf-core/nextflowpipelineutils/meta.yml new file mode 100644 index 00000000..f56b827b --- /dev/null +++ b/subworkflows/nf-core/nextflowpipelineutils/meta.yml @@ -0,0 +1,34 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "nextflow_pipeline_utils" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - out: + type: boolean + description: | + Dummy output for making using in process chaining. +authors: + - "@adamrtalbot" + - "@drpatelh" diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test new file mode 100644 index 00000000..db757ed1 --- /dev/null +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test @@ -0,0 +1,70 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/nextflowpipelineutils/main.nf" + tag 'subworkflows' + tag 'nextflowpipelineutils' + tag 'subworkflows/nextflowpipelineutils' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + when { + function { + """ + // no inputs + """ + } + } + + then { + assert function.success + assert snapshot(function.result).match() + } + + } + + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assert function.success + assert function.result =~ /publish_dir_mode/ + assert function.result =~ /copy/ + } + + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + when { + function { + """ + // no inputs + """ + } + } + + then { + assert function.success + assert snapshot(function.result).match() + } + + } + +} \ No newline at end of file diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap new file mode 100644 index 00000000..956bfac7 --- /dev/null +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap @@ -0,0 +1,12 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "" + ], + "timestamp": "2023-10-12T17:09:20.935733" + }, + "Test Function checkCondaChannels": { + "content": null, + "timestamp": "2023-10-12T17:09:24.933468" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test new file mode 100644 index 00000000..3cf7f034 --- /dev/null +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test @@ -0,0 +1,104 @@ +nextflow_workflow { + + name "Test Workflow NEXTFLOW_PIPELINE_UTILS" + script "../main.nf" + config "subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config" + workflow "NEXTFLOW_PIPELINE_UTILS" + tag 'subworkflows' + tag 'nextflowpipelineutils' + tag 'subworkflows/nextflowpipelineutils' + + test("Should run no inputs") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + input[0] = false + input[1] = false + input[2] = null + input[3] = false + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + + test("Should print version") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + input[0] = true + input[1] = false + input[2] = null + input[3] = false + """ + } + } + + then { + assert workflow.success + assert workflow.stdout.contains("nextflow_workflow v9.9.9") + } + + } + + + test("Should dump params") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = false + input[1] = true + input[2] = params.outdir + input[3] = false + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + + test("Should not create params JSON if no output directory") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = false + input[1] = true + input[2] = null + input[3] = false + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out, path(params.outdir).list()).match() + } + + } + +} diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap new file mode 100644 index 00000000..08040fd4 --- /dev/null +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.workflow.nf.test.snap @@ -0,0 +1,44 @@ +{ + "Should not create params JSON if no output directory": { + "content": [ + { + "0": [ + true + ], + "out": [ + true + ] + }, + [ + + ] + ], + "timestamp": "2023-10-13T11:55:54.576748" + }, + "Should dump params": { + "content": [ + { + "0": [ + true + ], + "out": [ + true + ] + } + ], + "timestamp": "2023-10-13T11:55:52.711329" + }, + "Should run no inputs": { + "content": [ + { + "0": [ + true + ], + "out": [ + true + ] + } + ], + "timestamp": "2023-10-13T11:55:49.048315" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config new file mode 100644 index 00000000..035c0f5d --- /dev/null +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.4' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} \ No newline at end of file From 135c6447e3b1ada4e84aa03e25beaa8e0b0276fd Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Oct 2023 15:22:32 +0200 Subject: [PATCH 152/175] tags --- .../fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml | 2 ++ subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml | 2 ++ 2 files changed, 4 insertions(+) create mode 100644 subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml create mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml new file mode 100644 index 00000000..ab064503 --- /dev/null +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml @@ -0,0 +1,2 @@ +fastq_download_prefetch_fasterqdump_sratools: + - subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/** diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml b/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml new file mode 100644 index 00000000..57127a2a --- /dev/null +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml @@ -0,0 +1,2 @@ +nextflowpipelineutils: + - subworkflows/nf-core/nextflowpipelineutils/** From a12c5a3b2452de4b16fb1d03b91f85ea81eacd0c Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 16 Oct 2023 15:51:54 +0200 Subject: [PATCH 153/175] Use nf-core nfvalidation subworkflow --- modules.json | 5 + .../local/nf_core_fetchngs_utils/main.nf | 4 +- .../local/nf_validation_plugin_utils/main.nf | 52 ----- .../nf-core/nfvalidation_plugin_utils/main.nf | 62 ++++++ .../nfvalidation_plugin_utils/meta.yml | 49 +++++ .../tests/main.nf.test | 199 ++++++++++++++++++ .../tests/main.nf.test.snap | 26 +++ .../tests/nextflow_schema.json | 96 +++++++++ 8 files changed, 439 insertions(+), 54 deletions(-) delete mode 100644 subworkflows/local/nf_validation_plugin_utils/main.nf create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/main.nf create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json diff --git a/modules.json b/modules.json index 3cc9d6dd..b8801dc6 100644 --- a/modules.json +++ b/modules.json @@ -38,6 +38,11 @@ "branch": "master", "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3", "installed_by": ["subworkflows"] + }, + "nfvalidation_plugin_utils": { + "branch": "master", + "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6", + "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index fd0e9855..05f9a2ba 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -9,8 +9,8 @@ */ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../modules/nf-core/custom/dumpsoftwareversions' -include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main' -include { NF_VALIDATION_PLUGIN_UTILS } from '../nf_validation_plugin_utils' +include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main' +include { NF_VALIDATION_PLUGIN_UTILS } from '../../nf-core/nfvalidation_plugin_utils/main.nf' include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils' /* diff --git a/subworkflows/local/nf_validation_plugin_utils/main.nf b/subworkflows/local/nf_validation_plugin_utils/main.nf deleted file mode 100644 index be815a7f..00000000 --- a/subworkflows/local/nf_validation_plugin_utils/main.nf +++ /dev/null @@ -1,52 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow NF_VALIDATION_PLUGIN_UTILS { - - take: - print_help // bool - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // bool - - main: - - // - // Print help message if needed - // - if (print_help && workflow_command) { - log.info pre_help_text + paramsHelp(workflow_command) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters() - } - - emit: - summary_params = paramsSummaryMap(workflow) -} diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf b/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf new file mode 100644 index 00000000..22531719 --- /dev/null +++ b/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf @@ -0,0 +1,62 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow NF_VALIDATION_PLUGIN_UTILS { + + take: + print_help // bool + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // bool: Validate parameters + schema_filename // path: JSON schema file, null to use default value + + main: + + log.debug "Using schema file: ${schema_filename}" + + // Default values for strings + pre_help_text = pre_help_text ?: '' + post_help_text = post_help_text ?: '' + workflow_command = workflow_command ?: '' + + // + // Print help message if needed + // + if (print_help) { + log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters(parameters_schema: schema_filename) + } + + summary_params = paramsSummaryMap(workflow, parameters_schema: schema_filename) + + emit: + summary_params = summary_params +} diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml b/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml new file mode 100644 index 00000000..6117b455 --- /dev/null +++ b/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml @@ -0,0 +1,49 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "nfvalidationpluginutils" +## TODO nf-core: Add a description of the subworkflow and list keywords +description: Sort SAM/BAM/CRAM file +keywords: + - sort + - bam + - sam + - cram +## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow +components: + - samtools/sort + - samtools/index +## TODO nf-core: List all of the channels used as input with a description and their structure +input: + - ch_bam: + type: file + description: | + The input channel containing the BAM/CRAM/SAM files + Structure: [ val(meta), path(bam) ] + pattern: "*.{bam/cram/sam}" +## TODO nf-core: List all of the channels used as output with a descriptions and their structure +output: + - bam: + type: file + description: | + Channel containing BAM files + Structure: [ val(meta), path(bam) ] + pattern: "*.bam" + - bai: + type: file + description: | + Channel containing indexed BAM (BAI) files + Structure: [ val(meta), path(bai) ] + pattern: "*.bai" + - csi: + type: file + description: | + Channel containing CSI files + Structure: [ val(meta), path(csi) ] + pattern: "*.csi" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@adamrtalbot" diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test new file mode 100644 index 00000000..6a0efd1e --- /dev/null +++ b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test @@ -0,0 +1,199 @@ +nextflow_workflow { + + name "Test Workflow NF_VALIDATION_PLUGIN_UTILS" + script "../main.nf" + workflow "NF_VALIDATION_PLUGIN_UTILS" + tag "subworkflow" + tag "subworkflow_nfcore" + tag "nfvalidationpluginutils" + tag "subworkflows/nfvalidationpluginutils" + + test("Should run nothing") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assert workflow.success + } + + } + + test("Should run help") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assert workflow.success + assert workflow.exitStatus == 0 + assert workflow.stdout.any { it.contains('Input/output options') } + assert workflow.stdout.any { it.contains('--outdir') } + assert workflow.stdout.any { it.contains('--outdir') } + } + + } + + test("Should run help with command") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assert workflow.success + assert workflow.exitStatus == 0 + assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } + assert workflow.stdout.any { it.contains('Input/output options') } + assert workflow.stdout.any { it.contains('--outdir') } + assert workflow.stdout.any { it.contains('--outdir') } + } + + } + + test("Should run help with extra text") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = "pre-help-text" + post_help_text = "post-help-text" + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assert workflow.success + assert workflow.exitStatus == 0 + assert workflow.stdout.any { it.contains('pre-help-text') } + assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } + assert workflow.stdout.any { it.contains('Input/output options') } + assert workflow.stdout.any { it.contains('--outdir') } + assert workflow.stdout.any { it.contains('--outdir') } + assert workflow.stdout.any { it.contains('post-help-text') } + } + + } + + test("Should validate params") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = true + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assert workflow.failed + assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } + assert workflow.stdout.any { it.contains('The following invalid input values have been detected:') } + } + + } + +} diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap new file mode 100644 index 00000000..ae33a930 --- /dev/null +++ b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test.snap @@ -0,0 +1,26 @@ +{ + "Should run help": { + "content": [ + { + "stderr": [ + + ], + "errorReport": "", + "exitStatus": 0, + "failed": false, + "stdout": [ + + ], + "errorMessage": "", + "trace": { + "tasksFailed": 0, + "tasksCount": 0, + "tasksSucceeded": 0 + }, + "name": "workflow", + "success": true + } + ], + "timestamp": "2023-10-13T13:18:16.933251413" + } +} diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json new file mode 100644 index 00000000..7626c1c9 --- /dev/null +++ b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "definitions": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} From 94d75cb01b0545a4cc2edf992e073a83707990fb Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:00:54 +0200 Subject: [PATCH 154/175] fix --- subworkflows/local/nf_core_fetchngs_utils/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index 05f9a2ba..f20bdbe7 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -44,7 +44,8 @@ workflow PIPELINE_INITIALISATION { workflow_command, pre_help_text, post_help_text, - params.validate_params + params.validate_params, + "nextflow_schema.json" ) // From f372eeb771adfb48cda42d42704e92b7876dc1b7 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:06:50 +0200 Subject: [PATCH 155/175] Use nf-core subworkflow: NFCORE_PIPELINE_UTILS --- modules.json | 5 + .../local/nf_core_fetchngs_utils/main.nf | 14 +- .../nfcore_pipeline_utils}/main.nf | 5 +- .../nf-core/nfcore_pipeline_utils/meta.yml | 17 +++ .../tests/main.function.nf.test | 120 ++++++++++++++++++ .../tests/main.function.nf.test.snap | 78 ++++++++++++ .../tests/main.workflow.nf.test | 33 +++++ .../tests/nextflow.config | 9 ++ 8 files changed, 277 insertions(+), 4 deletions(-) rename subworkflows/{local/nf_core_pipeline_utils => nf-core/nfcore_pipeline_utils}/main.nf (99%) create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/meta.yml create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config diff --git a/modules.json b/modules.json index 3cc9d6dd..d6f5a884 100644 --- a/modules.json +++ b/modules.json @@ -38,6 +38,11 @@ "branch": "master", "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3", "installed_by": ["subworkflows"] + }, + "nfcore_pipeline_utils": { + "branch": "master", + "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37", + "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index fd0e9855..f3035b58 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -9,9 +9,17 @@ */ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../modules/nf-core/custom/dumpsoftwareversions' -include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main' +include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main' include { NF_VALIDATION_PLUGIN_UTILS } from '../nf_validation_plugin_utils' -include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils' +include { + NFCORE_PIPELINE_UTILS; + workflowCitation; + nfCoreLogo; + dashedLine; + completionEmail; + completionSummary; + imNotification +} from '../../nf-core/nf_core_pipeline_utils' /* ======================================================================================== @@ -50,7 +58,7 @@ workflow PIPELINE_INITIALISATION { // // Check config provided to the pipeline // - NF_CORE_PIPELINE_UTILS () + NFCORE_PIPELINE_UTILS () // // Auto-detect input id type diff --git a/subworkflows/local/nf_core_pipeline_utils/main.nf b/subworkflows/nf-core/nfcore_pipeline_utils/main.nf similarity index 99% rename from subworkflows/local/nf_core_pipeline_utils/main.nf rename to subworkflows/nf-core/nfcore_pipeline_utils/main.nf index 18bf238b..b3b136dc 100644 --- a/subworkflows/local/nf_core_pipeline_utils/main.nf +++ b/subworkflows/nf-core/nfcore_pipeline_utils/main.nf @@ -8,11 +8,14 @@ ======================================================================================== */ -workflow NF_CORE_PIPELINE_UTILS { +workflow NFCORE_PIPELINE_UTILS { main: checkConfigProvided() + emit: + success = true + } /* diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml b/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml new file mode 100644 index 00000000..5721b7e3 --- /dev/null +++ b/subworkflows/nf-core/nfcore_pipeline_utils/meta.yml @@ -0,0 +1,17 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "NFCORE_PIPELINE_UTILS" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: [] +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test new file mode 100644 index 00000000..265ece39 --- /dev/null +++ b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test @@ -0,0 +1,120 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + when { + function { + """ + // define inputs of the function here. Example: + // input[0] = 1 + """ + } + } + + then { + assertAll ( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + + } + + test("Test Function workflowCitation") { + + function "workflowCitation" + + when { + function { + """ + // define inputs of the function here. Example: + // input[0] = 1 + """ + } + } + + then { + assertAll ( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + + } + + test("Test Function nfCoreLogo") { + + function "nfCoreLogo" + + when { + function { + """ + input[0] = "9.9.9" + """ + } + } + + then { + assertAll ( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + + } + + + + test("Test Function dashedLine") { + + function "dashedLine" + + when { + function { + """ + // define inputs of the function here. Example: + // input[0] = 1 + """ + } + } + + then { + assertAll ( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + + } + + + + test("Test Function logColours") { + + function "logColours" + + when { + function { + """ + // define inputs of the function here. Example: + // input[0] = 1 + """ + } + } + + then { + assertAll ( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap new file mode 100644 index 00000000..3ea51f68 --- /dev/null +++ b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.function.nf.test.snap @@ -0,0 +1,78 @@ +{ + "Test Function logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "timestamp": "2023-10-16T14:27:09.843064" + }, + "Test Function checkConfigProvided": { + "content": null, + "timestamp": "2023-10-16T14:27:01.415849" + }, + "Test Function nfCoreLogo": { + "content": [ + "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow 9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" + ], + "timestamp": "2023-10-16T14:27:51.566211" + }, + "Test Function workflowCitation": { + "content": [ + "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" + ], + "timestamp": "2023-10-16T14:27:03.505737" + }, + "Test Function dashedLine": { + "content": [ + "-\u001b[2m----------------------------------------------------\u001b[0m-" + ], + "timestamp": "2023-10-16T14:27:07.721916" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test new file mode 100644 index 00000000..ad7c73a8 --- /dev/null +++ b/subworkflows/nf-core/nfcore_pipeline_utils/tests/main.workflow.nf.test @@ -0,0 +1,33 @@ +nextflow_workflow { + + name "Test Workflow NFCORE_PIPELINE_UTILS" + script "../main.nf" + config "subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config" + workflow "NFCORE_PIPELINE_UTILS" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "nfcorepipelineutils" + tag "subworkflows/nfcorepipelineutils" + + test("Should run without failures") { + + when { + params { + // define parameters here. Example: + // outdir = "tests/results" + } + workflow { + """ + // define inputs of the workflow here. Example: + // input[0] = file("test-file.txt") + """ + } + } + + then { + assert workflow.success + } + + } + +} diff --git a/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config b/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config new file mode 100644 index 00000000..53574ffe --- /dev/null +++ b/subworkflows/nf-core/nfcore_pipeline_utils/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} \ No newline at end of file From 86cfae283941445a1d748a16669032e42cdee7e8 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:12:01 +0200 Subject: [PATCH 156/175] Update nextflowpipelineutils --- modules.json | 2 +- .../nextflowpipelineutils/tests/main.functions.nf.test | 1 + .../nextflowpipelineutils/tests/main.functions.nf.test.snap | 4 ++-- .../nf-core/nextflowpipelineutils/tests/nextflow.config | 2 +- subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml | 2 -- 5 files changed, 5 insertions(+), 6 deletions(-) delete mode 100644 subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml diff --git a/modules.json b/modules.json index 3cc9d6dd..ecd043f9 100644 --- a/modules.json +++ b/modules.json @@ -36,7 +36,7 @@ }, "nextflowpipelineutils": { "branch": "master", - "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3", + "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf", "installed_by": ["subworkflows"] } } diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test index db757ed1..1a1577eb 100644 --- a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test @@ -3,6 +3,7 @@ nextflow_function { name "Test Functions" script "subworkflows/nf-core/nextflowpipelineutils/main.nf" + config "subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config" tag 'subworkflows' tag 'nextflowpipelineutils' tag 'subworkflows/nextflowpipelineutils' diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap index 956bfac7..939dbbad 100644 --- a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap @@ -1,9 +1,9 @@ { "Test Function getWorkflowVersion": { "content": [ - "" + "v9.9.9" ], - "timestamp": "2023-10-12T17:09:20.935733" + "timestamp": "2023-10-15T13:43:55.128868" }, "Test Function checkCondaChannels": { "content": null, diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config index 035c0f5d..53574ffe 100644 --- a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config +++ b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.4' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } \ No newline at end of file diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml b/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml deleted file mode 100644 index 57127a2a..00000000 --- a/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -nextflowpipelineutils: - - subworkflows/nf-core/nextflowpipelineutils/** From 4464c07f301ecafea93ae83a624c3730f290daca Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:13:46 +0200 Subject: [PATCH 157/175] path fix --- subworkflows/local/nf_core_fetchngs_utils/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index f3035b58..b964ab5b 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -19,7 +19,7 @@ include { completionEmail; completionSummary; imNotification -} from '../../nf-core/nf_core_pipeline_utils' +} from '../../nf-core/nfcore_pipeline_utils' /* ======================================================================================== From 52c4100dbc5ddb0d0950a8f68ff3a4a78cd2e847 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:19:52 +0200 Subject: [PATCH 158/175] Update subworkflows/local/nf_core_fetchngs_utils/main.nf Co-authored-by: Maxime U Garcia --- subworkflows/local/nf_core_fetchngs_utils/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index b964ab5b..376f999e 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -9,7 +9,7 @@ */ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../modules/nf-core/custom/dumpsoftwareversions' -include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main' +include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main' include { NF_VALIDATION_PLUGIN_UTILS } from '../nf_validation_plugin_utils' include { NFCORE_PIPELINE_UTILS; From 16ce425f0afad8b0bb7f957704284fbfee0449b1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Oct 2023 16:15:35 +0200 Subject: [PATCH 159/175] update modules --- modules.json | 23 ++++--- .../sratoolsncbisettings/tests/tags.yml | 2 + modules/nf-core/untar/main.nf | 63 +++++++++++++++++++ modules/nf-core/untar/meta.yml | 41 ++++++++++++ 4 files changed, 120 insertions(+), 9 deletions(-) create mode 100644 modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml create mode 100644 modules/nf-core/untar/main.nf create mode 100644 modules/nf-core/untar/meta.yml diff --git a/modules.json b/modules.json index 7bf618ff..e5e6bbc6 100644 --- a/modules.json +++ b/modules.json @@ -7,23 +7,28 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", + "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5", "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { "branch": "master", - "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", + "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/fasterqdump": { "branch": "master", - "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", + "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/prefetch": { "branch": "master", - "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", + "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + }, + "untar": { + "branch": "master", + "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", + "installed_by": ["modules"] } } }, @@ -31,7 +36,7 @@ "nf-core": { "fastq_download_prefetch_fasterqdump_sratools": { "branch": "master", - "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", + "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5", "installed_by": ["subworkflows"] }, "nextflowpipelineutils": { @@ -39,14 +44,14 @@ "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf", "installed_by": ["subworkflows"] }, - "nfvalidation_plugin_utils": { + "nfcore_pipeline_utils": { "branch": "master", - "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6", + "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37", "installed_by": ["subworkflows"] }, - "nfcore_pipeline_utils": { + "nfvalidation_plugin_utils": { "branch": "master", - "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37", + "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml b/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml new file mode 100644 index 00000000..fb4a08a7 --- /dev/null +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml @@ -0,0 +1,2 @@ +custom/sratoolsncbisettings: + - modules/nf-core/custom/sratoolsncbisettings/** diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf new file mode 100644 index 00000000..61461c39 --- /dev/null +++ b/modules/nf-core/untar/main.nf @@ -0,0 +1,63 @@ +process UNTAR { + tag "$archive" + label 'process_single' + + conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("$prefix"), emit: untar + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) + + """ + mkdir $prefix + + ## Ensures --strip-components only applied when top level of tar contents is a directory + ## If just files or multiple directories, place all in prefix + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + tar \\ + -C $prefix --strip-components 1 \\ + -xavf \\ + $args \\ + $archive \\ + $args2 + else + tar \\ + -C $prefix \\ + -xavf \\ + $args \\ + $archive \\ + $args2 + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) + """ + mkdir $prefix + touch ${prefix}/file.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml new file mode 100644 index 00000000..db241a6e --- /dev/null +++ b/modules/nf-core/untar/meta.yml @@ -0,0 +1,41 @@ +name: untar +description: Extract files. +keywords: + - untar + - uncompress + - extract +tools: + - untar: + description: | + Extract tar.gz files. + documentation: https://www.gnu.org/software/tar/manual/ + licence: ["GPL-3.0-or-later"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - untar: + type: directory + description: Directory containing contents of archive + pattern: "*/" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@matthdsm" + - "@jfy133" From 5875c57588cafd1f9f3389be3a2842bbf33c0f00 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Oct 2023 16:18:55 +0200 Subject: [PATCH 160/175] patch custom-dumpsoftwareversions snap --- .../custom-dumpsoftwareversions.diff | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff new file mode 100644 index 00000000..307c06ea --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff @@ -0,0 +1,49 @@ +Changes in module 'nf-core/custom/dumpsoftwareversions' +--- /dev/null ++++ modules/nf-core/custom/dumpsoftwareversions/nextflow.config +@@ -0,0 +1,10 @@ ++process { ++ withName: CUSTOM_DUMPSOFTWAREVERSIONS { ++ cache = false ++ publishDir = [ ++ path: { "${params.outdir}/pipeline_info" }, ++ mode: params.publish_dir_mode, ++ pattern: '*_versions.yml' ++ ] ++ } ++} +--- modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap ++++ modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +@@ -3,25 +3,25 @@ + "content": [ + { + "0": [ +- "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" ++ "software_versions.yml:md5,45e271267967cd582c53d2cc609f8e02" + ], + "1": [ +- "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" ++ "software_versions_mqc.yml:md5,2b6b639f9edde0b032afcd9d2fcf6877" + ], + "2": [ + "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + ], + "mqc_yml": [ +- "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" ++ "software_versions_mqc.yml:md5,2b6b639f9edde0b032afcd9d2fcf6877" + ], + "versions": [ + "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + ], + "yml": [ +- "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" ++ "software_versions.yml:md5,45e271267967cd582c53d2cc609f8e02" + ] + } + ], +- "timestamp": "2023-10-11T17:10:02.930699" ++ "timestamp": "2023-10-17T16:16:58.324012" + } +-} ++} +************************************************************ From 4312b74fface24c1069826c402ac343719a991d6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Oct 2023 16:33:44 +0200 Subject: [PATCH 161/175] update snaps --- .../custom/dumpsoftwareversions/tests/main.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap index 8713b921..c4e7a6d3 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -22,6 +22,6 @@ ] } ], - "timestamp": "2023-10-11T17:10:02.930699" + "timestamp": "2023-10-17T16:16:58.324012" } -} +} \ No newline at end of file From 2f47befc1d66324ecbddd06bf184a5e2b645b1ae Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 17 Oct 2023 16:43:48 +0200 Subject: [PATCH 162/175] Replace CUSTOM_DUMPSOFTWAREVERSIONS with collectFile operator --- modules.json | 13 +-- .../custom/dumpsoftwareversions/main.nf | 24 ----- .../custom/dumpsoftwareversions/meta.yml | 36 ------- .../dumpsoftwareversions/nextflow.config | 10 -- .../templates/dumpsoftwareversions.py | 101 ------------------ .../dumpsoftwareversions/tests/main.nf.test | 38 ------- .../tests/main.nf.test.snap | 27 ----- .../dumpsoftwareversions/tests/tags.yml | 2 - .../local/nf_core_fetchngs_utils/main.nf | 12 ++- 9 files changed, 12 insertions(+), 251 deletions(-) delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/nextflow.config delete mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml diff --git a/modules.json b/modules.json index 7bf618ff..81b6b318 100644 --- a/modules.json +++ b/modules.json @@ -5,11 +5,6 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", - "installed_by": ["modules"] - }, "custom/sratoolsncbisettings": { "branch": "master", "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", @@ -39,14 +34,14 @@ "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf", "installed_by": ["subworkflows"] }, - "nfvalidation_plugin_utils": { + "nfcore_pipeline_utils": { "branch": "master", - "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6", + "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37", "installed_by": ["subworkflows"] }, - "nfcore_pipeline_utils": { + "nfvalidation_plugin_utils": { "branch": "master", - "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37", + "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf deleted file mode 100644 index c9d014b1..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_single' - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.15" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - template 'dumpsoftwareversions.py' -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml deleted file mode 100644 index c32657de..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,36 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - dump - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" - -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - -authors: - - "@drpatelh" - - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/nextflow.config b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config deleted file mode 100644 index 241654e7..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/nextflow.config +++ /dev/null @@ -1,10 +0,0 @@ -process { - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100755 index da033408..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,101 +0,0 @@ -#!/usr/bin/env python - - -"""Provide functions to merge multiple versions.yml files.""" - - -import yaml -import platform -from textwrap import dedent - - -def _make_versions_html(versions): - """Generate a tabular HTML output of all versions for MultiQC.""" - html = [ - dedent( - """\\ - - - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
Process Name Software Version
{process if (i == 0) else ''}{tool}{version}
") - return "\\n".join(html) - - -def main(): - """Load all version files and generate merged output.""" - versions_this_module = {} - versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, - } - - with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - - # aggregate versions by the module name (derived from fully-qualified process name) - versions_by_module = {} - for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), - } - - with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) - with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) - - -if __name__ == "__main__": - main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test deleted file mode 100644 index eec1db10..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ /dev/null @@ -1,38 +0,0 @@ -nextflow_process { - - name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "../main.nf" - process "CUSTOM_DUMPSOFTWAREVERSIONS" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "dumpsoftwareversions" - tag "custom/dumpsoftwareversions" - - test("Should run without failures") { - when { - process { - """ - def tool1_version = ''' - TOOL1: - tool1: 0.11.9 - '''.stripIndent() - - def tool2_version = ''' - TOOL2: - tool2: 1.9 - '''.stripIndent() - - input[0] = Channel.of(tool1_version, tool2_version).collectFile() - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap deleted file mode 100644 index 8713b921..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ /dev/null @@ -1,27 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" - ], - "1": [ - "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" - ], - "2": [ - "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" - ], - "mqc_yml": [ - "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" - ], - "versions": [ - "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" - ], - "yml": [ - "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" - ] - } - ], - "timestamp": "2023-10-11T17:10:02.930699" - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24a..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index eecc62e1..287ed0db 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -8,7 +8,6 @@ ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../modules/nf-core/custom/dumpsoftwareversions' include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main' include { NF_VALIDATION_PLUGIN_UTILS } from '../../nf-core/nfvalidation_plugin_utils/main.nf' include { @@ -113,9 +112,14 @@ workflow PIPELINE_COMPLETION { // // MODULE: Dump software versions for all tools used in the workflow // - CUSTOM_DUMPSOFTWAREVERSIONS ( - versions.collectFile(name: 'collated_versions.yml') - ) + pipeline_version_info = Channel.of(""" + "Workflow": + "Nextflow": ${workflow.nextflow.version}, + "${workflow.manifest.name}": ${workflow.manifest.version}, + """.stripIndent()) + + versions = versions.mix(pipeline_version_info) + versions.collectFile(name: 'versions.yml', storeDir: "${params.outdir}/pipeline_info") // // Completion email and summary From f941c4db34d66547ce2bcafd90638138ba3388d4 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 17 Oct 2023 16:46:28 +0200 Subject: [PATCH 163/175] fixup --- nextflow.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index 3589e118..f7674569 100644 --- a/nextflow.config +++ b/nextflow.config @@ -65,9 +65,6 @@ try { System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } -// Module specific configs -includeConfig './modules/nf-core/custom/dumpsoftwareversions/nextflow.config' - // Workflow specific configs if (params.input_type == 'sra') { includeConfig './workflows/sra/nextflow.config' From ba1924327a061d594fed190b610ef2307a11f3d0 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 17 Oct 2023 17:10:23 +0200 Subject: [PATCH 164/175] gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index ff233cdb..ef809d7c 100644 --- a/.gitignore +++ b/.gitignore @@ -4,6 +4,7 @@ .nf-test.log data/ nf-test +.nf-test* results/ test.xml testing* From 364e6baf05fdcc3f60f963361cfcb9a999c8707a Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 17 Oct 2023 17:16:08 +0200 Subject: [PATCH 165/175] Use software versions file that matches MultiQC input --- subworkflows/local/nf_core_fetchngs_utils/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index 287ed0db..f07e7997 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -119,7 +119,7 @@ workflow PIPELINE_COMPLETION { """.stripIndent()) versions = versions.mix(pipeline_version_info) - versions.collectFile(name: 'versions.yml', storeDir: "${params.outdir}/pipeline_info") + versions.collectFile(name: 'fetchngs_mqc_versions.yml', storeDir: "${params.outdir}/pipeline_info") // // Completion email and summary From e6c79c557ab1ce39533c4fe063abcebf20a3b31e Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 17 Oct 2023 17:29:21 +0200 Subject: [PATCH 166/175] tidy --- subworkflows/local/nf_core_fetchngs_utils/main.nf | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf index f07e7997..509a4473 100644 --- a/subworkflows/local/nf_core_fetchngs_utils/main.nf +++ b/subworkflows/local/nf_core_fetchngs_utils/main.nf @@ -112,10 +112,9 @@ workflow PIPELINE_COMPLETION { // // MODULE: Dump software versions for all tools used in the workflow // - pipeline_version_info = Channel.of(""" - "Workflow": - "Nextflow": ${workflow.nextflow.version}, - "${workflow.manifest.name}": ${workflow.manifest.version}, + pipeline_version_info = Channel.of("""\"workflow\": + nextflow: ${workflow.nextflow.version} + ${workflow.manifest.name}: ${workflow.manifest.version} """.stripIndent()) versions = versions.mix(pipeline_version_info) From a9d8ae875c5797c137ca80eb6f8833299aff2ab9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Oct 2023 17:50:16 +0200 Subject: [PATCH 167/175] forgot patch --- modules.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules.json b/modules.json index e5e6bbc6..4966f053 100644 --- a/modules.json +++ b/modules.json @@ -8,7 +8,8 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff" }, "custom/sratoolsncbisettings": { "branch": "master", From cedd600b2e8de83a5671d8b3c0fd803571039063 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Oct 2023 17:57:37 +0200 Subject: [PATCH 168/175] add data --- conf/test_data.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/test_data.config b/conf/test_data.config index 68e84262..670115a8 100644 --- a/conf/test_data.config +++ b/conf/test_data.config @@ -24,6 +24,12 @@ params { } test_data { + 'sarscov2'{ + 'illumina' { + SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" + SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" + } + } 'generic' { 'config' { ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg" From 5884bba8db03ffb58fc6e2fb00e33d602e13fb1b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Oct 2023 10:32:07 +0200 Subject: [PATCH 169/175] tinier tests + patch fasterdump --- modules.json | 3 ++- .../nf-core/sratools/fasterqdump/tests/main.nf.test.snap | 4 ++-- tests/sra_ids_test.csv | 6 +----- workflows/sra/tests/main.nf.test | 2 +- workflows/sra/tests/sra_force_sratools_download.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- .../sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test | 2 +- workflows/sra/tests/sra_skip_fastq_download.nf.test | 2 +- 10 files changed, 12 insertions(+), 15 deletions(-) diff --git a/modules.json b/modules.json index 7fa9eaf0..81312b77 100644 --- a/modules.json +++ b/modules.json @@ -13,7 +13,8 @@ "sratools/fasterqdump": { "branch": "master", "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5", - "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"], + "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff" }, "sratools/prefetch": { "branch": "master", diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap index d3bf90f7..77fd6c79 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "test_single_end", "single_end": true }, - "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" + "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" ] ], "1": [ @@ -20,7 +20,7 @@ "id": "test_single_end", "single_end": true }, - "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" + "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" ] ], "versions": [ diff --git a/tests/sra_ids_test.csv b/tests/sra_ids_test.csv index ec8b5cc9..d9a20c22 100644 --- a/tests/sra_ids_test.csv +++ b/tests/sra_ids_test.csv @@ -1,7 +1,3 @@ -SRR9984183 -SRR13191702 ERR1160846 -SRR12848126 -SRR14593545 -SRR14709033 GSE214215 +SRR12848126 diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index c234e98f..ef5b7c9d 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') """ } params { diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index e2d4f54f..df751a6b 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 0e2fcac3..f4837f76 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 5f8d37a2..871207ab 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 95bbe2c8..995301dd 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 21c78ae7..4bf6a3f0 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') """ } params { diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index bcc4b697..705facbb 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') """ } params { From b9a8609be309ce629073775baaf92a9de02457c5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Oct 2023 10:33:13 +0200 Subject: [PATCH 170/175] diff file --- .../fasterqdump/sratools-fasterqdump.diff | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff diff --git a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff new file mode 100644 index 00000000..5275d3e4 --- /dev/null +++ b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff @@ -0,0 +1,36 @@ +Changes in module 'nf-core/sratools/fasterqdump' +--- /dev/null ++++ modules/nf-core/sratools/fasterqdump/nextflow.config +@@ -0,0 +1,10 @@ ++process { ++ withName: SRATOOLS_FASTERQDUMP { ++ ext.args = '--split-files --include-technical' ++ publishDir = [ ++ path: { "${params.outdir}/fastq" }, ++ mode: params.publish_dir_mode, ++ pattern: "*.fastq.gz" ++ ] ++ } ++} +--- modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap ++++ modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap +@@ -8,7 +8,7 @@ + "id": "test_single_end", + "single_end": true + }, +- "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" ++ "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" + ] + ], + "1": [ +@@ -20,7 +20,7 @@ + "id": "test_single_end", + "single_end": true + }, +- "test_single_end.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" ++ "test_single_end_1.fastq.gz:md5,1054c7b71884acdb5eed8a378f18be82" + ] + ], + "versions": [ + +************************************************************ From 0d5f1d00097695baaae733f9930532b7374a52a0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Oct 2023 10:33:27 +0200 Subject: [PATCH 171/175] one last test --- workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 62bb1999..62cabb7b 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') + input[0] = Channel.from('ERR1160846', 'GSE214215', 'SRR12848126') """ } params { From b885d5252b5f0b30bde28615d58c82e666fbf2db Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 18 Oct 2023 11:35:25 +0200 Subject: [PATCH 172/175] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9fbb2013..8a9459c4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,7 +24,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Enhancements & fixes -- [PR #XXX](https://github.com/nf-core/fetchngs/pull/XXX) - Use nf-test for all pipeline testing +- [PR #188](https://github.com/nf-core/fetchngs/pull/188) - Use nf-test for all pipeline testing ### Enhancements & fixes From 79487642f2ecd8ef058f1104e59af9f184971960 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Oct 2023 11:36:56 +0200 Subject: [PATCH 173/175] Prepare 1.11.0 RC --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c500efcc..4247dde3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [Unpublished Version / DEV] +## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18 ### Enhancements & fixes diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index a8974f98..21e8296b 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/fetchngs + This report has been generated by the nf-core/fetchngs analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-fetchngs-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 912ce43c..c7d78f99 100644 --- a/nextflow.config +++ b/nextflow.config @@ -220,7 +220,7 @@ manifest { description = """Pipeline to fetch metadata and raw FastQ files from public databases""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.11.0dev' + version = '1.11.0' doi = 'https://doi.org/10.5281/zenodo.5070524' } From 833ad7eb79a67801d536c767f6c6272cc7fd566f Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Wed, 18 Oct 2023 09:51:04 +0000 Subject: [PATCH 174/175] qwqUpdate snaps --- workflows/sra/tests/main.nf.test.snap | 14 +++++++------- .../sra_custom_ena_metadata_fields.nf.test.snap | 14 +++++++------- .../tests/sra_force_sratools_download.nf.test.snap | 14 +++++++------- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 14 +++++++------- .../tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 14 +++++++------- .../sra_nf_core_pipeline_taxprofiler.nf.test.snap | 14 +++++++------- .../sra_nf_core_pipeline_viralrecon.nf.test.snap | 14 +++++++------- .../sra/tests/sra_skip_fastq_download.nf.test.snap | 14 +++++++------- 8 files changed, 56 insertions(+), 56 deletions(-) diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 4ba15917..885b7d6a 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac" + "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2" ], "2": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "3": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac" + "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-13T13:45:55.621951" + "timestamp": "2023-10-18T09:49:19.020482551" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 5e98f3b1..45e007d0 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,4ea86d2a38bf25d025331afd1925a138" + "samplesheet.csv:md5,a9e9da506288c364af14d46b86dafeb1" ], "2": [ - "id_mappings.csv:md5,e581a9117ed2cc8e98e65c25fe7f34aa" + "id_mappings.csv:md5,8ed2bd72d432eff4a8ed7d909af6f60c" ], "3": [ [ - "multiqc_config.yml:md5,0f18d574c7ddfa08cf444a593cb91cde", + "multiqc_config.yml:md5,3bc981f0de28023083cdf13691d249d5", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,e581a9117ed2cc8e98e65c25fe7f34aa" + "id_mappings.csv:md5,8ed2bd72d432eff4a8ed7d909af6f60c" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,0f18d574c7ddfa08cf444a593cb91cde", + "multiqc_config.yml:md5,3bc981f0de28023083cdf13691d249d5", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,4ea86d2a38bf25d025331afd1925a138" + "samplesheet.csv:md5,a9e9da506288c364af14d46b86dafeb1" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-13T13:41:56.570144" + "timestamp": "2023-10-18T09:36:57.154883885" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 1c92c75d..f445296a 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,461dfaa7b95f84210840347ef8cc93c2" + "samplesheet.csv:md5,7e6a65057fe000f562132ae9e608e87b" ], "2": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "3": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -28,16 +28,16 @@ ], "mappings": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,461dfaa7b95f84210840347ef8cc93c2" + "samplesheet.csv:md5,7e6a65057fe000f562132ae9e608e87b" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -48,6 +48,6 @@ ] } ], - "timestamp": "2023-10-13T13:51:26.617172" + "timestamp": "2023-10-18T09:43:16.468494798" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index cabe296e..3e9e7f31 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,0deebc93328dcbb63762aa91d4fc9f35" + "samplesheet.csv:md5,35292d2bea78b087d75c3333f6319b6b" ], "2": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "3": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,0deebc93328dcbb63762aa91d4fc9f35" + "samplesheet.csv:md5,35292d2bea78b087d75c3333f6319b6b" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-13T13:37:42.486986" + "timestamp": "2023-10-18T09:47:56.240260295" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 111fe537..8805d3ac 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,e20d0858b2ff04a62d50274a2527b913" + "samplesheet.csv:md5,b7ac0ff84f5031daaa9405c736a37125" ], "2": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "3": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,e20d0858b2ff04a62d50274a2527b913" + "samplesheet.csv:md5,b7ac0ff84f5031daaa9405c736a37125" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-13T13:43:56.980991" + "timestamp": "2023-10-18T09:40:15.590249346" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index 14c38837..0853eef8 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,c781b226b9aac812c1d38881145a74d6" + "samplesheet.csv:md5,296836917bbdf34bda106a313424fa95" ], "2": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "3": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,c781b226b9aac812c1d38881145a74d6" + "samplesheet.csv:md5,296836917bbdf34bda106a313424fa95" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-13T13:39:55.31037" + "timestamp": "2023-10-18T09:49:51.04235046" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index d26dd1cc..e364b3a9 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac" + "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2" ], "2": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "3": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -29,16 +29,16 @@ ], "mappings": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,5926f40ded37e0e6ce0b290c445772ac" + "samplesheet.csv:md5,eda595eca3cb5ed450641565c38390c2" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -50,6 +50,6 @@ ] } ], - "timestamp": "2023-10-13T13:35:41.371352" + "timestamp": "2023-10-18T09:48:46.587502263" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index f0bac51f..cdb0965c 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -6,14 +6,14 @@ ], "1": [ - "samplesheet.csv:md5,23d39235ed39f69cb8333322de77ed26" + "samplesheet.csv:md5,0a9b99509bcc64ca245408b6bb634f15" ], "2": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "3": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], @@ -27,16 +27,16 @@ ], "mappings": [ - "id_mappings.csv:md5,57116724ccf0215795b44d4458e6861f" + "id_mappings.csv:md5,3e70c965568c59f8c8fbb8e99e7a8b79" ], "sample_mappings": [ [ - "multiqc_config.yml:md5,77050a65c8ad23e5b052b576bff1eeff", + "multiqc_config.yml:md5,6d4c3e5137704358474330207f5f2b5c", "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" ] ], "samplesheet": [ - "samplesheet.csv:md5,23d39235ed39f69cb8333322de77ed26" + "samplesheet.csv:md5,0a9b99509bcc64ca245408b6bb634f15" ], "versions": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", @@ -46,6 +46,6 @@ ] } ], - "timestamp": "2023-10-13T13:46:11.136377" + "timestamp": "2023-10-18T09:50:04.300075498" } } \ No newline at end of file From 4d13a4470639a9ae6a84610f900f9d97e276ce03 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 18 Oct 2023 11:56:39 +0200 Subject: [PATCH 175/175] Update .github/workflows/ci.yml Co-authored-by: Maxime U Garcia --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2268c794..53480a37 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,7 +10,6 @@ on: branches: - master - dev - - refactor env: NXF_ANSI_LOG: false